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Das R, Mishra P, Mishra B, Jha R. Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens. J Anim Sci Biotechnol 2024; 15:62. [PMID: 38702804 PMCID: PMC11069197 DOI: 10.1186/s40104-024-01022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17th embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21. RESULTS The results were considered significantly different at P < 0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d 21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto 1 in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21. CONCLUSION In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.
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Affiliation(s)
- Razib Das
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Pravin Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Rajesh Jha
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
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K I, Y M, A N, D S, G G, R S, D G, V SN, O S, M F, S R, S O, J MG, A M. Cognitive behavioral and mindfulness with daily exercise intervention is associated with changes in intestinal microbial taxa and systemic inflammation in patients with Crohn's disease. Gut Microbes 2024; 16:2337269. [PMID: 38591914 PMCID: PMC11005811 DOI: 10.1080/19490976.2024.2337269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease associated with psychological distress and intestinal microbial changes. Here, we examined whether a 3-month period of Cognitive Behavioral and Mindfulness with Daily Exercise (COBMINDEX) intervention, which improves the wellbeing and inflammatory state of CD patients, may also affect their gut microbiome. Gut microbiota, circulating inflammatory markers and hormones were analyzed in 24 CD patients before (T1) and after 3 months of COBMINDEX (T2), and in 25 age- and sex-matched wait-list control patients at the corresponding time-points. Microbiota analysis examined relative taxonomical abundance, alpha and beta diversity, and microbiome correlations with inflammatory and psychological parameters. At T1, CD patients exhibited a characteristic microbial profile mainly constituted of Proteobacteria (17.71%), Firmicutes (65.56%), Actinobacteria (8.46%) and Bacteroidetes (6.24%). Baseline bacterial abundances showed significant correlations with psychological markers of distress and with IFNγ . Following COBMINDEX, no significant changes in alpha and beta diversity were observed between both study groups, though a trend change in beta diversity was noted. Significant changes occurred in the abundance of phyla, families and genera only among the COBMINDEX group. Furthermore, abundance of phyla, families and genera that were altered following COBMNIDEX, significantly correlated with levels of cytokines and psychological parameters. Our results demonstrated that a short-term intervention of COBMINDEX was associated with changes in microbial indices, some of which are linked to psychological manifestations and systemic inflammation in CD patients. Psychological interventions to reduce chronic stress, such as COBMINDEX, appear to be beneficial in mitigating the pathobiology of CD patients, and may thus provide a useful adjunct to pharmacological therapy.
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Affiliation(s)
- Ilan K
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Motro Y
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Nemirovsky A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Schwartz D
- Department of Gastroenterology and Hepatology, Soroka Medical Center, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Goren G
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sergienko R
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Greenberg D
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Slonim-Nevo V
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sarid O
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Friger M
- Department of Epidemiology, Biostatistics and Community Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Regev S
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Odes S
- Department of Gastroenterology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moran-Gilad J
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Monsonego A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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3
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Conn KA, Borsom EM, Cope EK. Implications of microbe-derived ɣ-aminobutyric acid (GABA) in gut and brain barrier integrity and GABAergic signaling in Alzheimer's disease. Gut Microbes 2024; 16:2371950. [PMID: 39008552 PMCID: PMC11253888 DOI: 10.1080/19490976.2024.2371950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
The gut microbial ecosystem communicates bidirectionally with the brain in what is known as the gut-microbiome-brain axis. Bidirectional signaling occurs through several pathways including signaling via the vagus nerve, circulation of microbial metabolites, and immune activation. Alterations in the gut microbiota are implicated in Alzheimer's disease (AD), a progressive neurodegenerative disease. Perturbations in gut microbial communities may affect pathways within the gut-microbiome-brain axis through altered production of microbial metabolites including ɣ-aminobutyric acid (GABA), the primary inhibitory mammalian neurotransmitter. GABA has been shown to act on gut integrity through modulation of gut mucins and tight junction proteins and may be involved in vagus nerve signal inhibition. The GABAergic signaling pathway has been shown to be dysregulated in AD, and may be responsive to interventions. Gut microbial production of GABA is of recent interest in neurological disorders, including AD. Bacteroides and Lactic Acid Bacteria (LAB), including Lactobacillus, are predominant producers of GABA. This review highlights how temporal alterations in gut microbial communities associated with AD may affect the GABAergic signaling pathway, intestinal barrier integrity, and AD-associated inflammation.
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Affiliation(s)
- Kathryn A. Conn
- Center for Applied Microbiome Sciences, The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily M. Borsom
- Center for Data-Driven Discovery for Biology, Allen Institute, Seattle, WA, USA
| | - Emily K. Cope
- Center for Applied Microbiome Sciences, The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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Fetter K, Weigel M, Ott B, Fritzenwanker M, Stricker S, de Laffolie J, Hain T. The microbiome landscape in pediatric Crohn's disease and therapeutic implications. Gut Microbes 2023; 15:2247019. [PMID: 37614093 PMCID: PMC10453987 DOI: 10.1080/19490976.2023.2247019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
Dysbiosis of the gut microbiome and a pathological immune response in intestinal tissues form the basis of Crohn's disease (CD), which is a debilitating disease with relevant morbidity and mortality. It is increasing in childhood and adolescents, due to western life-style and nutrition and a large set of predisposing genetic factors. Crohn's disease-associated genetic mutations play an essential role in killing pathogens, altering mucosal barrier function, and protecting the host microbiome, suggesting an important pathogenic link. The intestinal microbiome is highly variable and can be influenced by environmental factors. Changes in microbial composition and a reduction in species diversity have been shown to be central features of disease progression and are therefore the target of therapeutic approaches. In this review, we summarize the current literature on the role of the gut microbiome in childhood, adolescent, and adult CD, current therapeutic options, and their impact on the microbiome.
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Affiliation(s)
- Karin Fetter
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Markus Weigel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Benjamin Ott
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Moritz Fritzenwanker
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sebastian Stricker
- Department of Pediatrics, Justus Liebig University Giessen, Giessen, Germany
| | - Jan de Laffolie
- Department of Pediatrics, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
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5
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Van Pee T, Nawrot TS, van Leeuwen R, Hogervorst J. Ambient particulate air pollution and the intestinal microbiome; a systematic review of epidemiological, in vivo and, in vitro studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162769. [PMID: 36907413 DOI: 10.1016/j.scitotenv.2023.162769] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 05/13/2023]
Abstract
A healthy indigenous intestinal microbiome is indispensable for intra- and extra-intestinal human health. Since well-established factors such as diet and antibiotic use only explain 16 % of the inter-individual variation in gut microbiome composition, recent studies have focused on the association between ambient particulate air pollution and the intestinal microbiome. We systematically summarize and discuss all evidence concerning the effect of particulate air pollution on intestinal bacterial diversity indices, specific bacterial taxa, and potential underlying intestinal mechanisms. To this end, all possibly relevant publications published between February 1982 and January 2023 were screened, and eventually, 48 articles were included. The vast majority (n = 35) of these studies were animal studies. The exposure periods investigated in the human epidemiological studies (n = 12) ranged from infancy through elderly. This systematic review found that intestinal microbiome diversity indices were generally negatively associated with particulate air pollution in epidemiological studies, with an increase in taxa belonging to Bacteroidetes (two studies), Deferribacterota (one study), and Proteobacteria (four studies), a decrease in taxa belonging to Verrucomicrobiota (one study), and no consensus for taxa belonging to Actinobacteria (six studies) and Firmicutes (seven studies). There was no unequivocal effect of ambient particulate air pollution exposure on bacterial indices and taxa in animal studies. Only one study in humans examined a possible underlying mechanism; yet, the included in vitro and animal studies depicted higher gut damage, inflammation, oxidative stress, and permeability in exposed versus unexposed animals. Overall, the population-based studies showed a dose-related continuum of short- and long-term ambient particulate air pollution exposure on lower gut diversity and shifts in taxa over the entire life course.
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Affiliation(s)
- Thessa Van Pee
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium; Department of Public Health and Primary Care, Leuven University, Herestraat 49-box 706, 3000 Leuven, Belgium.
| | - Romy van Leeuwen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Janneke Hogervorst
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
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6
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Van Pee T, Nawrot TS, van Leeuwen R, Hogervorst J. The Gut Microbiome and Residential Surrounding Greenness: a Systematic Review of Epidemiological Evidence. Curr Environ Health Rep 2023:10.1007/s40572-023-00398-4. [PMID: 37296363 DOI: 10.1007/s40572-023-00398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 06/12/2023]
Abstract
PURPOSE OF REVIEW A healthy indigenous intestinal microbiome is essential for human health. Well-established gut microbiome determinants only explain 16% of the inter-individual variation in gut microbiome composition. Recent studies have focused on green space as a potential determinant of the intestinal microbiome. We systematically summarize all evidence concerning the association between green space and intestinal bacterial diversity, evenness, and richness indices, specific bacterial taxa, and potential underlying mechanisms. RECENT FINDINGS Seven epidemiological studies were included in this review. The majority of the included studies (n = 4) reported a positive association between green space and intestinal bacterial diversity, evenness, and richness, while two reported the opposite. There was little overlap between the publications regarding the association between green space and the relative abundance of specific bacterial taxa. Only a decrease in the relative abundance of Bacteroidetes, Bacteroides, and Anaerostipes and an increase in Lachnospiraceae and Ruminococcaceae were reported in multiple studies, predominantly suggesting that green space is positively associated with the intestinal microbiome composition, and subsequently with human health. Lastly, the only examined mechanism was a reduction in perceived psychosocial stress. Mechanisms indicated in blue and white represent tested or hypothesized mechanisms, respectively. The graphical abstract was created with illustrations from BioRender, Noun Project, and Pngtree.
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Affiliation(s)
- Thessa Van Pee
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
- Department of Public Health and Primary Care, Leuven University, Herestraat 49-Box 706, 3000, Louvain, Belgium.
| | - Romy van Leeuwen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Janneke Hogervorst
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
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7
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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8
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Dysbiosis in Inflammatory Bowel Disease: Pathogenic Role and Potential Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23073464. [PMID: 35408838 PMCID: PMC8998182 DOI: 10.3390/ijms23073464] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Microbe-host communication is essential to maintain vital functions of a healthy host, and its disruption has been associated with several diseases, including Crohn's disease and ulcerative colitis, the two major forms of inflammatory bowel disease (IBD). Although individual members of the intestinal microbiota have been associated with experimental IBD, identifying microorganisms that affect disease susceptibility and phenotypes in humans remains a considerable challenge. Currently, the lack of a definition between what is healthy and what is a dysbiotic gut microbiome limits research. Nevertheless, although clear proof-of-concept of causality is still lacking, there is an increasingly evident need to understand the microbial basis of IBD at the microbial strain, genomic, epigenomic, and functional levels and in specific clinical contexts. Recent information on the role of diet and novel environmental risk factors affecting the gut microbiome has direct implications for the immune response that impacts the development of IBD. The complexity of IBD pathogenesis, involving multiple distinct elements, suggests the need for an integrative approach, likely utilizing computational modeling of molecular datasets to identify more specific therapeutic targets.
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Karunakaran G, Yang Y, Tremblay V, Ning Z, Martin J, Belaouad A, Figeys D, Brunzelle J, Giguere PM, Stintzi A, Couture JF. Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease. FEBS Lett 2022; 596:898-909. [PMID: 35122247 DOI: 10.1002/1873-3468.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022]
Abstract
Crohn's Disease (CD) is characterized by the chronic inflammation of the gastrointestinal tract. A dysbiotic microbiome and a defective immune system are linked to CD, where hydrogen sulfide (H2 S) microbial producers positively correlate with the severity of the disease. Atopobium parvulum is a key H2 S producer from the microbiome of CD patients. In this study, the biochemical characterization of two Atopobium parvulum cysteine desulfurases, ApSufS and ApCsdB, show that the enzymes are allosterically regulated. Structural analyses reveal that ApSufS forms a dimer with conserved characteristics observed in type II cysteine desulfurases. Four residues surrounding the active site are essential to catalyze cysteine desulfurylation, and a segment of short-chain residues grant access for substrate binding. A better understanding of ApSufS will help future avenues for CD treatment.
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Affiliation(s)
- Gapisha Karunakaran
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Yidai Yang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Véronique Tremblay
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jade Martin
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Amine Belaouad
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Joseph Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, 60611, USA
| | - Patrick M Giguere
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
| | - Jean-François Couture
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Faculty of Medicine, Ottawa, ON, Canada
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10
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Lyu Z, Yu T, Zhang L, Xu X, Zhang Y, Li J, Li Z, Zhang W, Hou S. Analysis of the relationship between bile duct and duodenal microbiota reveals that potential dysbacteriosis is the main cause of primary common bile duct stones. Synth Syst Biotechnol 2021; 6:414-428. [PMID: 34901480 PMCID: PMC8632725 DOI: 10.1016/j.synbio.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/21/2021] [Accepted: 11/07/2021] [Indexed: 01/30/2023] Open
Abstract
Bacteria play an important role in the formation of primary Common Bile Duct (CBD) stones. However, the composition and function of the microbiota of bile duct in patients with primary CBD stones remained to be explored. We utilized the 16S rRNA gene high-throughput sequencing technology to analyze the microbial diversity and community composition of biliary and duodenal microbiota in 15 patients with primary CBD stones and 4 patients without biliary tract diseases. Alpha diversity analysis showed that the microbiota richness was similar in bile and intestinal fluid; Beta diversity analysis showed that there were differences in the composition between biliary microbiota and the duodenal microbiota, but the abundance of the main groups showed similarities. The composition of the biliary microbiota from gallstone patients was more complex, as was the duodenal microbiota. Proteobacteria and Firmicutes were the dominant bacteria at phylum level, accounting for at least 75% of the total reads in each subgroup. Pseudomonas and Escherichia-Shigella were the major genus among subgroups, but Escherichia-Shigella had increased abundance in duodenal microbiota with primary choledocholithiasis, which may play an important role in stone formation. It is noteworthy that Clostridiumsensu_stricto, Lachnospiraceae _UCG-008, Butyrivibrio and Roseburia which could produce short chain fatty acids (SCFAs), were significantly decreased in biliary microbiota with primary CBD stones (p < 0.05). Our study provided new insights into the compositional of normal biliary microbiota. The micro-ecology of biliary and duodenal in patients with stones is complex and closely related, and there is a potential for dysbacteriosis. The decrease in abundance of certain major acid-producing bacteria affects the health of the biliary tract and thus leads to the formation of stones.
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Affiliation(s)
- Zhitang Lyu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, PR China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, PR China.,Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Baoding, PR China
| | - Tingting Yu
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Lichao Zhang
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Xiaona Xu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, PR China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, PR China
| | - Yijun Zhang
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, PR China.,Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, PR China
| | - Jihong Li
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Zhirong Li
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Wei Zhang
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
| | - Senlin Hou
- The Second Hospital of Hebei Medical University, Shijiazhuang, PR China
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Liu S, Luorong Q, Hu K, Cao W, Tao W, Liu H, Zhang D. Aqueous Extract of Lysimachia christinae Hance Prevents Cholesterol Gallstone in Mice by Affecting the Intestinal Microflora. J Microbiol Biotechnol 2021; 31:1272-1280. [PMID: 34261853 PMCID: PMC9706107 DOI: 10.4014/jmb.2106.06043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022]
Abstract
With changes in human dietary patterns, the proportion of high-fat and high-cholesterol foods in the daily diet has increased. As a result, the incidence rate of cholelithiasis is increasing rapidly. Many studies have reported on the crucial role that the intestinal microflora plays in the progression of gallstones. Although the whole herb of Lysimachia christinae, a traditional Chinese medicine, has long been extensively used as a remedy for cholelithiasis in China, its effects on the intestinal microflora remain unknown. Hence, in this study, we investigated the ability of the aqueous extract of L. christinae (LAE) to prevent cholesterol gallstones (CGSs) in model animals by affecting the intestinal microflora. The effects of LAE on body weight, serum lipid profile, visceral organ indexes, and histomorphology were studied in male C57BL/6J mice, which were induced by a lithogenic diet. After the 8-week study, CGSs formation was greatly reduced after LAE treatment. LAE also reduced body weight gain and hyperlipidemia and restored the histomorphological changes. Moreover, the intestinal microflora exhibited significant variation. In the model group fed the lithogenic diet, the abundances of the genera unclassified Porphyromonadaceae, Lactobacillus and Alloprevotella decreased, but in contrast, Akkermansia dramatically increased compared with the control check group, which was fed a normal diet; the administration of LAE reversed these changes. These results imply that L. christinae can be considered an efficient therapy for eliminating CGSs induced by a high-fat and high-cholesterol diet, which may be achieved by influencing the intestinal microflora.
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Affiliation(s)
- Shijia Liu
- First Clinical College, Chongqing Medical University, Chongqing 400016, P.R.China
| | - Quji Luorong
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, P.R.China
| | - Kaizhi Hu
- Chongqing Institute of Pharmaceutical Plant, Chongqing 408435, P.R.China
| | - Weiguo Cao
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, P.R.China
| | - Wei Tao
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, P.R.China
| | - Handeng Liu
- Laboratory of Tissue and Cell Biology, Experimental Teaching Center, Chongqing Medical University, Chongqing 400016, P.R.China,Molecular Medicine and Cancer Research Center, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, P.R.China,Corresponding authors H. Liu Phone: +86-23-6571-2090 E-mail:
| | - Dan Zhang
- College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, P.R.China,
D. Zhang Phone: +86-23-6370-2109 E-mail: zhangdan01234567@ hotmail.com
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12
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Otten AT, Bourgonje AR, Peters V, Alizadeh BZ, Dijkstra G, Harmsen HJM. Vitamin C Supplementation in Healthy Individuals Leads to Shifts of Bacterial Populations in the Gut-A Pilot Study. Antioxidants (Basel) 2021; 10:antiox10081278. [PMID: 34439526 PMCID: PMC8389205 DOI: 10.3390/antiox10081278] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbes are crucial to human health, but microbial composition is often disturbed in a number of human diseases. Accumulating evidence points to nutritional modulation of the gut microbiota as a potentially beneficial therapeutic strategy. Vitamin C (ascorbic acid) may be of particular interest as it has known antioxidant and anti-inflammatory properties. In this study, we investigated whether supplementation with high-dose vitamin C may favourably affect the composition of the gut microbiota. In this pilot study, healthy human participants received 1000 mg vitamin C supplementation daily for two weeks. Gut microbiota composition was analysed before and after intervention by performing faecal 16S rRNA gene sequencing. In total, 14 healthy participants were included. Daily supplementation of high-dose vitamin C led to an increase in the relative abundances of Lachnospiraceae (p < 0.05), whereas decreases were observed for Bacteroidetes (p < 0.01), Enterococci (p < 0.01) and Gemmiger formicilis (p < 0.05). In addition, trends for bacterial shifts were observed for Blautia (increase) and Streptococcus thermophilus (decrease). High-dose vitamin C supplementation for two weeks shows microbiota-modulating effects in healthy individuals, with several beneficial shifts of bacterial populations. This may be relevant as these bacteria have anti-inflammatory properties and strongly associate with gut health.
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Affiliation(s)
- Antonius T. Otten
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Vera Peters
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Correspondence: ; Tel.: +31-50-361-3480
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13
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Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients. Appl Microbiol Biotechnol 2021; 105:3277-3288. [PMID: 33839797 PMCID: PMC8053167 DOI: 10.1007/s00253-021-11264-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 03/25/2021] [Accepted: 04/04/2021] [Indexed: 02/06/2023]
Abstract
Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: • Comparison of gut microbiota and mycobiota between IBS and healthy subjects • Investigation of cultivable fungi in IBS and healthy subjects • Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.
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14
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The Western Dietary Pattern Combined with Vancomycin-Mediated Changes to the Gut Microbiome Exacerbates Colitis Severity and Colon Tumorigenesis. Nutrients 2021; 13:nu13030881. [PMID: 33803094 PMCID: PMC8000903 DOI: 10.3390/nu13030881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Previous work by our group using a mouse model of inflammation-associated colorectal cancer (CAC) showed that the total Western diet (TWD) promoted colon tumor development. Others have also shown that vancomycin-mediated changes to the gut microbiome increased colorectal cancer (CRC). Therefore, the objective of this study was to determine the impact of vancomycin on colon tumorigenesis in the context of a standard mouse diet or the TWD. A 2 × 2 factorial design was used, in which C57Bl/6J mice were fed either the standard AIN93G diet or TWD and with vancomycin in the drinking water or not. While both the TWD and vancomycin treatments independently increased parameters associated with gut inflammation and tumorigenesis compared to AIN93G and plain water controls, mice fed the TWD and treated with vancomycin had significantly increased tumor multiplicity and burden relative to all other treatments. Vancomycin treatment significantly decreased alpha diversity and changed the abundance of several taxa at the phylum, family, and genus levels. Conversely, basal diet had relatively minor effects on the gut microbiome composition. These results support our previous research that the TWD promotes colon tumorigenesis and suggest that vancomycin-induced changes to the gut microbiome are associated with higher tumor rates.
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15
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Revilla L, Mayorgas A, Corraliza AM, Masamunt MC, Metwaly A, Haller D, Tristán E, Carrasco A, Esteve M, Panés J, Ricart E, Lozano JJ, Salas A. Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis. PLoS One 2021; 16:e0246367. [PMID: 33556098 PMCID: PMC7870068 DOI: 10.1371/journal.pone.0246367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease. RESULTS We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis. CONCLUSIONS The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
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Affiliation(s)
- Lluís Revilla
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Ana M. Corraliza
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Maria C. Masamunt
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Eva Tristán
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Anna Carrasco
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Julian Panés
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Elena Ricart
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Juan J. Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
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16
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Babakhanov AT, Dzhumabekov AT, Zhao AV, Kuandykov YK, Tanabayeva SB, Fakhradiyev IR, Nazarenko Y, Saliev TM. Impact of Appendectomy on Gut Microbiota. Surg Infect (Larchmt) 2021; 22:651-661. [PMID: 33523761 DOI: 10.1089/sur.2020.422] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Considered vestigial from the classic point of view, the vermiform appendix has long been the subject of intensive studies. The recent understanding of appendix function in the context of unique architecture and bacterial complexity and density allows considering it as a safehouse for intestinal biodiversity. Methods: This review analyzes and assesses the current state of scientific knowledge regarding the role of the vermiform appendix in normal gut microbiota maintenance as a crucial factor of host homeostasis. It also highlights the difference in microbial composition between the large bowel and the appendix, as well as the association between the surgical excision, appendectomy, and dysbiosis-induced diseases. In addition, the review discusses the results of epidemiologic studies on appendectomy as a risk factor for the initiation of gastrointestinal carcinogenesis. It also highlights the association between appendectomy and a series of chronic inflammatory and neurologic disorders, including inflammatory bowel disease.
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Affiliation(s)
| | | | - Alexey V Zhao
- Institute of Surgery named after A.V. Vishnevsky, Moscow, Russia
| | - Yerlan K Kuandykov
- Khoja Akhmet Yassawi International Kazakh-Turkish University, Shymkent Medical Institute Postgraduate Studies Faculty, Shymkent, Kazakhstan
| | | | | | - Yana Nazarenko
- S.D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Timur M Saliev
- S.D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
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17
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Vaga S, Lee S, Ji B, Andreasson A, Talley NJ, Agréus L, Bidkhori G, Kovatcheva-Datchary P, Park J, Lee D, Proctor G, Ehrlich SD, Nielsen J, Engstrand L, Shoaie S. Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals. Sci Rep 2020; 10:14977. [PMID: 32917913 PMCID: PMC7486370 DOI: 10.1038/s41598-020-71939-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.
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Affiliation(s)
- Stefania Vaga
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden
- Department of Psychology, Macquarie University, Macquarie Park, NSW, Australia
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | | | - Lars Agréus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Gholamreza Bidkhori
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Petia Kovatcheva-Datchary
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345, Gothenburg, Sweden
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Scientific Research Center for Translational Medicine, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Junseok Park
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | | | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- BioInnovation Institute, Ole Maaløes Vej 3, 2200, Copenhagen N, Denmark.
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, & Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK.
- Science for Life Laboratory, KTH-Royal Institute of Technology, Tomtebodavägen 23A, 17165, Solna, Sweden.
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18
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Differential miRNA-Gene Expression in M Cells in Response to Crohn's Disease-Associated AIEC. Microorganisms 2020; 8:microorganisms8081205. [PMID: 32784656 PMCID: PMC7466023 DOI: 10.3390/microorganisms8081205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC), which abnormally colonize the ileal mucosa of Crohn’s disease (CD) patients, are able to invade intestinal epithelial cells (IECs) and translocate through M cells overlying Peyer’s patches. The levels of microRNA (miRNA) and gene expression in IECs and M cells upon AIEC infection have not been investigated. Here, we used human intestinal epithelial Caco-2 monolayers and an in vitro M-cell model of AIEC translocation to analyze comprehensive miRNA and gene profiling under basal condition and upon infection with the reference AIEC LF82 strain. Our results showed that AIEC LF82 translocated through M cells but not Caco-2 monolayers. Both differential gene expression and miRNA profile in M cells compared to Caco-2 cells were obtained. In addition, AIEC infection induces changes in gene and miRNA profiles in both Caco-2 and M cells. In silico analysis showed that certain genes dysregulated upon AIEC infection were potential targets of AIEC-dysregulated miRNAs, suggesting a miRNA-mediated regulation of gene expression during AIEC infection in Caco-2, as well as M cells. This study facilitates the discovery of M cell-specific and AIEC response-specific gene-miRNA signature and enhances the molecular understanding of M cell biology under basal condition and in response to infection with CD-associated AIEC.
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19
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Silver nanoparticles based on blackcurrant extract show potent anti-inflammatory effect in vitro and in DSS-induced colitis in mice. Int J Pharm 2020; 585:119549. [PMID: 32554032 DOI: 10.1016/j.ijpharm.2020.119549] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022]
Abstract
Silver nanoparticles have been used in a range of applications and although they are already employed in medicine, there are new, promising possibilities for their utilization. We investigated the potential of silver nanoparticles obtained with the use of blackcurrant extract in vitro in the LPS-stimulated RAW264.7 macrophages and in vivo in the murine DSS-induced colitis model. The examined formulations contained particles of 95 nm (Ag95) and 213 nm (Ag213) diameter. In vitro, both formulations inhibited nitric oxide (NO) release. In vivo, the preparations alleviated colitis as evidenced by a decreased macroscopic score and myeloperoxidase activity (indicative of neutrophil infiltration). In both cases, the nanoparticles of larger diameter showed better anti-inflammatory properties. Although further tests are required, our results indicate a plausible new use of silver nanoparticles in inflammatory bowel diseases.
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20
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Misra BB. The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research. Biol Res Nurs 2020; 22:561-576. [PMID: 32013533 DOI: 10.1177/1099800420903083] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Big data-driven omics research has led to a steep rise in investigations involving two of the most functional omes, the metabolome and microbiome. The former is touted as the closest to the phenotype, and the latter is implicated in general well-being and a plethora of human diseases. Although some research publications have integrated the concepts of the two domains, most focus their analyses on evidence solely originating from one or the other. With a growing interest in connecting the microbiome and metabolome in the context of disease, researchers must also appreciate the disconnect between the two domains. In the present review, drawing examples from the current literature, tools, and resources, I discuss the connections between the microbiome and metabolome and highlight challenges and opportunities in linking them together for the basic, translational, clinical, and nursing research communities.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, 12279Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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21
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Brown TA, Tashiro H, Kasahara DI, Cho Y, Shore SA. Early life microbiome perturbation alters pulmonary responses to ozone in male mice. Physiol Rep 2020; 8:e14290. [PMID: 31981310 PMCID: PMC6981302 DOI: 10.14814/phy2.14290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Early life changes in the microbiome contribute to the development of allergic asthma, but little is known about the importance of the microbiome for other forms of asthma. Ozone is a nonatopic asthma trigger that causes airway hyperresponsiveness and neutrophil recruitment to the lungs. The purpose of this study was to test the hypothesis that early life perturbations in the gut microbiome influence subsequent responses to ozone. To that end, we placed weanling mouse pups from The Jackson Laboratories or from Taconic Farms in sex-specific cages either with other mice from the same vendor (same-housed) or with mice from the opposite vendor (cohoused). Mice were maintained with these cagemates until use. The gut microbial community differs in mice from Jackson Labs and Taconic Farms, and cohousing mice transfers fecal microbiota from one mouse to another. Indeed, 16S rRNA sequencing of fecal DNA indicated that differences in the gut microbiomes of Jackson and Taconic same-housed mice were largely abolished when the mice were cohoused. At 10-12 weeks of age, mice were exposed to room air or ozone (2 ppm for 3 hr). Compared to same-housed mice, cohoused male but not female mice had reduced ozone-induced airway hyperresponsiveness and reduced ozone-induced increases in bronchoalveolar lavage neutrophils. Ozone-induced airway hyperresponsiveness was greater in male than in female mice and the sex difference was largely abolished in cohoused mice. The data indicate a role for early life microbial perturbations in pulmonary responses to a nonallergic asthma trigger.
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Affiliation(s)
- Traci A. Brown
- Molecular and Integrative Physiological Sciences ProgramDepartment of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Hiroki Tashiro
- Molecular and Integrative Physiological Sciences ProgramDepartment of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - David I. Kasahara
- Molecular and Integrative Physiological Sciences ProgramDepartment of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Youngji Cho
- Molecular and Integrative Physiological Sciences ProgramDepartment of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Stephanie A. Shore
- Molecular and Integrative Physiological Sciences ProgramDepartment of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
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22
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Goulet O, Hojsak I, Kolacek S, Pop TL, Cokugras FC, Zuccotti G, Pettoello‐Mantovani M, Fabiano V. Paediatricians play a key role in preventing early harmful events that could permanently influence the development of the gut microbiota in childhood. Acta Paediatr 2019; 108:1942-1954. [PMID: 31197890 PMCID: PMC6852013 DOI: 10.1111/apa.14900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/14/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023]
Abstract
AIM The development of the gut microbiota occurs primarily during infancy, and growing evidence has emphasised its positive role and implications for human health. The aim of this review was to provide essential knowledge about the gut microbiota and to describe and highlight the importance of the factors that influence the gut microbiota in early life and their potential harmful effects later in life. METHODS The European Paediatric Association, the Union of the National European Paediatric Societies and Associations, convened a panel of independent European experts to summarise the research on microbiota for general paediatricians. They used PubMed and the Cochrane Library to identify studies published in English up to June 2018. RESULTS A number of clinical conditions can disrupt the development of a stable gut microbiota. Changes in the microbiome have been documented in many chronic diseases, mainly immune-mediated gastrointestinal and liver diseases, and distinct patterns have been associated with each specific disease. The gut microbiota can be positively modulated with probiotics, prebiotics, synbiotics, paraprobiotics and postbiotics. CONCLUSION Paediatricians can play a key role in preventing harmful events that could permanently influence the composition and/or function of the gut microbiota. Various treatment strategies can be used.
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Affiliation(s)
- Olivier Goulet
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Intestinal Failure Rehabilitation Centre, National Reference Centre for Rare Digestive Diseases, APHP Necker‐Enfants Malades HospitalParis‐Descartes UniversityParisFrance
| | - Iva Hojsak
- Children’s Hospital ZagrebUniversity of Zagreb School of MedicineZagrebCroatia
- School of MedicineUniversity J.J. StrossmayerOsijekCroatia
| | - Sanja Kolacek
- Children’s Hospital ZagrebUniversity of Zagreb School of MedicineZagrebCroatia
| | - Tudor Lucian Pop
- Second Paediatric ClinicUniversity of Medicine and Pharmacy Iuliu HatieganuCluj‐NapocaRomania
| | - Fugen Cullu Cokugras
- Paediatric Gastroenterology, Hepatology and Nutrition, Cerrahpas_a Medical FacultyIstanbul UniversityIstanbulTurkey
| | - Gianvincenzo Zuccotti
- Pediatric Department, Vittore Buzzi Children’s HospitalUniversità degli Studi di MilanoMilanItaly
| | - Massimo Pettoello‐Mantovani
- Department of Pediatrics, Scientific Institute ‘Casa Sollievo della Sofferenza’University of FoggiaFoggiaItaly
- European Paediatric Association/Union of National European Paediatric Societies and Associations (EPA/UNEPSA)BerlinGermany
| | - Valentina Fabiano
- Pediatric Department, Vittore Buzzi Children’s HospitalUniversità degli Studi di MilanoMilanItaly
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Qi Y, Lohman J, Bratlie KM, Peroutka-Bigus N, Bellaire B, Wannemuehler M, Yoon KJ, Barrett TA, Wang Q. Vitamin C and B 3 as new biomaterials to alter intestinal stem cells. J Biomed Mater Res A 2019; 107:1886-1897. [PMID: 31071241 PMCID: PMC6626554 DOI: 10.1002/jbm.a.36715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/12/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022]
Abstract
Vitamin C (ascorbic acid) and vitamin B3 (niacin) have been extensively studied since the 20th century. In the area of stem cell biology, vitamin C has shown its direct impact toward homeostasis and epigenetic changes (D'Aniello et al., Stem Cells International, 2017, 1-16). Vitamin B3 aids in maintaining healthy intestinal homeostasis and reducing gut inflammation by participating in the rapamycin signaling pathway (Kumar et al., The American Journal of Physiology-Gastrointestinal and Liver Physiology, 2013). In this study, vitamin C and vitamin B3 (600 and 1,200 μg/mL) have been explored as potential new biomaterials to study their effects on four types of intestinal stem cells which are isolated from mice bearing different microbiota. We observed that C3H ASF and 129 ASF IL-10 are more sensitive towardB7 600 μg/mL vitamin B3 and 1,200 μg/mL vitamin C. The lowest growth rate and viability for all types of organoids was with 1,200 μg/mL vitamin C. From quantitative polymerase chain reaction analysis (qPCR analysis), MUC2 was upregulated for 129 ASF and C3H Conv when exposed to 600 μg/mL and 1,200 μg/mL vitamin C. It suggests that large amounts of glycoprotein may be produced after adding high concentrations of vitamin C. Since inflammatory bowel disease has low level of MUC2, this finding may be helpful in restoring mucosal health by upregulating the MUC2 gene while altering patient's microbiota (Sibila et al., Annals of the American Thoracic Society, 2016). These results are expected to have a positive translational impact because this bottom-up strategy would be instrumental in developing Vitamin C and B3 based orally available therapeutic strategies and formula for advancing the fields of gastrointestinal regenerative medicine.
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Affiliation(s)
- Yijun Qi
- Department of Chemical and Biological Engineering, Iowa State University
| | - Jo Lohman
- Department of Chemical and Biological Engineering, Iowa State University
| | - Kaitlin M Bratlie
- Department of Chemical and Biological Engineering, Iowa State University
- Department of Materials Science and Engineering, Iowa State University
| | | | - Bryan Bellaire
- Department of Vet Microbiology and Preventive Medicine, Iowa State University
| | | | - Kyoung-Jin Yoon
- Department of Vet Diagnostic and Production Animal Medicine, Iowa State University
| | - Terrence A Barrett
- Department of Internal Medicine, Division of Gastroenterology, University of Kentucky
| | - Qun Wang
- Department of Chemical and Biological Engineering, Iowa State University
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Wawrzycki B, Pietrzak A, Grywalska E, Krasowska D, Chodorowska G, Roliński J. Interleukin-22 and Its Correlation with Disease Activity in Plaque Psoriasis. Arch Immunol Ther Exp (Warsz) 2019; 67:103-108. [PMID: 30291393 PMCID: PMC6420473 DOI: 10.1007/s00005-018-0527-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/17/2018] [Indexed: 02/07/2023]
Abstract
Psoriasis is a chronic debilitating skin disease with an estimated prevalence reaching 2% of the worldwide population. Psoriatic disease is driven by a network of complicated reciprocal interactions among innate and adaptive mechanisms of immune system with structural components of the skin. Interleukin (IL)-22 mediates keratinocyte proliferation and epidermal hyperplasia, inhibits terminal differentiation of keratinocytes, and induces the production of antimicrobial proteins. The aim of this study was the assessment of IL-22 levels and its correlation with disease activity in plaque psoriasis. The study group included 64 patients with mild, moderate and severe psoriasis. Control group was composed of 24 sex- and age-matched healthy volunteers. IL-22 concentration was assessed in supernatants of T-cell cultures as well as in the plasma of study and control group with the use of ELISA method. Statistical analysis showed that concentration of IL-22 in cultures exposed to staphylococcal enterotoxin B was significantly higher than in control samples (p = 0.005) and cultures treated with IL-12 (p = 0.005). Patients with psoriasis presented significantly higher concentrations of IL-22 than healthy individuals (p = 0.0000001). In conclusion, IL-22 may collaborate with other soluble factors and cells together forming inflammatory circuits that otherwise exist as constitutive or inducible pathways in normal skin and become pathologically amplificated in psoriasis. Targeting IL-22 may be promising as a potential therapeutic for plaque psoriasis.
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Affiliation(s)
- Bartłomiej Wawrzycki
- Department of Dermatology, Venereology and Pediatric Dermatology, Medical University of Lublin, Lublin, Poland
| | - Aldona Pietrzak
- Department of Dermatology, Venereology and Pediatric Dermatology, Medical University of Lublin, Lublin, Poland
| | - Ewelina Grywalska
- Department of Clinical Immunology and Immunotherapy, Medical University of Lublin, Chodzki 4a, 20-093, Lublin, Poland.
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Medical University of Lublin, Lublin, Poland
| | - Grażyna Chodorowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Medical University of Lublin, Lublin, Poland
| | - Jacek Roliński
- Department of Clinical Immunology and Immunotherapy, Medical University of Lublin, Chodzki 4a, 20-093, Lublin, Poland
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25
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A Small Aromatic Compound Has Antifungal Properties and Potential Anti-Inflammatory Effects against Intestinal Inflammation. Int J Mol Sci 2019; 20:ijms20020321. [PMID: 30646601 PMCID: PMC6359570 DOI: 10.3390/ijms20020321] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 02/02/2023] Open
Abstract
Resistance of the opportunistic pathogen Candida albicans to antifungal drugs has increased significantly in recent years. After screening 55 potential antifungal compounds from a chemical library, 2,3-dihydroxy-4-methoxybenzaldehyde (DHMB) was identified as having potential antifungal activity. The properties of DHMB were then assessed in vitro and in vivo against C. albicans overgrowth and intestinal inflammation. Substitution on the aromatic ring of DHMB led to a strong decrease in its biological activity against C. albicans. The MIC of DHMB was highly effective at eliminating C. albicans when compared to that of caspofungin or fluconazole. Additionally, DHMB was also effective against clinically isolated fluconazole- or caspofungin-resistant C. albicans strains. DHMB was administered to animals at high doses. This compound was not cytotoxic and was well-tolerated. In experimental dextran sodium sulphate (DSS)-induced colitis in mice, DHMB reduced the clinical and histological score of inflammation and promoted the elimination of C. albicans from the gut. This finding was supported by a decrease in aerobic bacteria while anaerobic bacteria populations were re-established in mice treated with DHMB. DHMB is a small organic molecule with antifungal properties and anti-inflammatory activity by exerting protective effects on intestinal epithelial cells.
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Abstract
Inflammatory bowel diseases (IBD), categorized as ulcerative colitis (UC), Crohn's disease (CD), or IBD-undetermined (IBDU), are increasing in incidence. IBD is understood to result from environmental factors interacting with a pre-existing genetic susceptibility. Approximately 1% of all patients with inflammatory bowel disease (IBD) are diagnosed before the age of 6 years, designated as very-early-onset IBD (VEOIBD). This cohort of patients is distinguished from other age groups by differences in disease phenotype and by a higher burden of genetic mutations. Recent studies have linked mutations in NADPH oxidase function to VEOIBD and even pediatric IBD. Loss-of-function NOX2 variants expressed in phagocytes and NOX1/DUOX2 variants expressed in intestinal epithelial cells have been associated with VEOIBD and pediatric and adult IBD in patients. Cell and animal studies suggest a protective role for these reactive oxygen species (ROS)-producing enzymes in intestinal homeostasis-a paradigm that challenges the conventional concept that only increased ROS result in cell and tissue damage. Examining the role of NADPH oxidases in VEOIBD may improve our understanding of the pathophysiology of this disease and will uncover new therapeutic possibilities.
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Affiliation(s)
- Emily Stenke
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Billy Bourke
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.,Department of Paediatric Gastroenterology, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.
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27
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Goethel A, Croitoru K, Philpott DJ. The interplay between microbes and the immune response in inflammatory bowel disease. J Physiol 2018; 596:3869-3882. [PMID: 29806140 DOI: 10.1113/jp275396] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/18/2022] Open
Abstract
The aetiology and pathogenesis of inflammatory bowel disease (IBD) remains unclear but involves a complex interplay between genetic risk, environmental exposures, the immune system and the gut microbiota. Nearly two decades ago, the first susceptibility gene for Crohn's disease, NOD2, was identified within the IBD 1 locus. Since then, over 230 genetic risk loci have been associated with IBD and yet NOD2 remains the strongest association to date. As an intracellular innate immune sensor of bacteria, investigations into host-microbe interactions, involving both innate and adaptive immune responses, have become of particular interest in understanding the pathogenesis of IBD. Advancements in sequencing technology have lead to the groundbreaking characterization of the gut microbiota and its role in health and disease. While an altered microbiome has been described for IBD, whether it is a cause or an effect of the intestinal inflammation has yet to be determined. Moreover, the bidirectional relationship between the gut microbiota and the mucosal immune system adds to the multifaceted complexity of intestinal homeostasis. A better understanding of how host genetics, including NOD2, influence immune-microbe interactions and alter susceptibility to IBD is necessary in order to develop therapeutic and preventative treatments.
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Affiliation(s)
- Ashleigh Goethel
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dana J Philpott
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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28
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Abstract
We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual’s specific microbiota. High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest. In this work we present selbal, a greedy stepwise algorithm for selection of balances or microbial signatures that preserves the principles of compositional data analysis. We illustrate the algorithm with 16S rRNA abundance data from a Crohn’s microbiome study and an HIV microbiome study. IMPORTANCE We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual’s specific microbiota.
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29
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Rivera-Pinto J, Egozcue JJ, Pawlowsky-Glahn V, Paredes R, Noguera-Julian M, Calle ML. Balances: a New Perspective for Microbiome Analysis. mSystems 2018. [PMID: 30035234 DOI: 10.1101/219386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest. In this work we present selbal, a greedy stepwise algorithm for selection of balances or microbial signatures that preserves the principles of compositional data analysis. We illustrate the algorithm with 16S rRNA abundance data from a Crohn's microbiome study and an HIV microbiome study. IMPORTANCE We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual's specific microbiota.
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Affiliation(s)
- J Rivera-Pinto
- irsiCaixa AIDS Research Institute, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - J J Egozcue
- Universitat Politècnica de Catalunya, Barcelona, Spain
| | | | - R Paredes
- irsiCaixa AIDS Research Institute, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
- Infectious Diseases Service, Hospital Germans Trias i Pujol, Badalona, Spain
| | - M Noguera-Julian
- irsiCaixa AIDS Research Institute, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
- Universitat Autónoma de Barcelona, Barcelona, Spain
| | - M L Calle
- Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
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30
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Marlicz W, Skonieczna-Żydecka K, Dabos KJ, Łoniewski I, Koulaouzidis A. Emerging concepts in non-invasive monitoring of Crohn's disease. Therap Adv Gastroenterol 2018; 11:1756284818769076. [PMID: 29707039 PMCID: PMC5912292 DOI: 10.1177/1756284818769076] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an umbrella term for Crohn's disease (CD) and ulcerative colitis (UC). In light of evolving epidemiology of CD, its clinical management is still complex and remains a challenge for contemporary physicians. With the advent of new diagnostic and treatment paradigms, there is a growing need for new biomarkers to guide decision-making, differential diagnosis, disease activity monitoring, as well as prognosis. However, both clinical and endoscopic scoring systems, widely utilized for disease monitoring and prognosis, have drawbacks and limitations. In recent years, biochemical peptides have become available for IBD monitoring and more frequently used as surrogate markers of gut inflammation. Emerging concepts that revolve around molecular, stem cell, epigenetic, microbial or metabolomic pathways associated with vascular and epithelial gut barrier could lead to development of new CD biomarkers. Measurement of cell-derived microvesicles (MVs) in the blood of IBD patients is another emerging concept helpful in future disease management. In this review, we discuss novel concepts of non-invasive biomarkers, which may become useful in monitoring of CD activity and prognosis. We discuss metabolomics as a new powerful tool for clinicians to guide differential IBD diagnosis. In the coming years, new developments of prognostic tools are expected, aiming for breakthroughs in the management of patients with CD.
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Affiliation(s)
- Wojciech Marlicz
- Department of Gastroenterology, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | | | | | - Igor Łoniewski
- Department of Biochemistry and Human Nutrition, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. K., Szczecin, Poland
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31
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Tandon D, Haque MM, R. S, Shaikh S, P. S, Dubey AK, Mande SS. A snapshot of gut microbiota of an adult urban population from Western region of India. PLoS One 2018; 13:e0195643. [PMID: 29624599 PMCID: PMC5889170 DOI: 10.1371/journal.pone.0195643] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/26/2018] [Indexed: 12/27/2022] Open
Abstract
The human gut microbiome contributes to a broad range of biochemical and metabolic functions that directly or indirectly affect human physiology. Several recent studies have indicated that factors like age, geographical location, genetic makeup, and individual health status significantly influence the diversity, stability, and resilience of the gut microbiome. Of the mentioned factors, geographical location (and related dietary/socio-economic context) appears to explain a significant portion of microbiome variation observed in various previously conducted base-line studies on human gut microbiome. Given this context, we have undertaken a microbiome study with the objective of cataloguing the taxonomic diversity of gut microbiomes sampled from an urban cohort from Ahmedabad city in Western India. Computational analysis of microbiome sequence data corresponding to 160 stool samples (collected from 80 healthy individuals at two time-points, 60 days apart) has indicated a Prevotella-dominated microbial community. Given that the typical diet of participants included carbohydrate and fibre-rich components (predominantly whole grains and legume-based preparations), results appear to validate the proposed correlation between diet/geography and microbiome composition. Comparative analysis of obtained gut microbiome profiles with previously published microbiome profiles from US, China, Finland, and Japan additionally reveals a distinct taxonomic and (inferred) functional niche for the sampled microbiomes.
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Affiliation(s)
- Disha Tandon
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Hadapsar Industrial Estate, Pune Maharashtra, India
| | - Mohammed Monzoorul Haque
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Hadapsar Industrial Estate, Pune Maharashtra, India
| | - Saravanan R.
- Tata Chemicals Ltd. Innovation Centre, Ambedveth, Mulshi, Pune, Maharashtra, India
| | - Shafiq Shaikh
- Veeda Clinical Research Pvt. Ltd. Near IIM, Ambawadi, Ahmedabad, Gujarat, India
| | - Sriram P.
- Genotypic Technology (P) Ltd., Poojari Layout, Bangalore, India
| | - Ashok Kumar Dubey
- Tata Chemicals Ltd. Innovation Centre, Ambedveth, Mulshi, Pune, Maharashtra, India
- * E-mail: (SSM); (AKD)
| | - Sharmila S. Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Hadapsar Industrial Estate, Pune Maharashtra, India
- * E-mail: (SSM); (AKD)
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32
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Chiodini RJ, Dowd SE, Barron JN, Galandiuk S, Davis B, Glassing A. Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn's disease of the terminal ileum. J Med Microbiol 2018; 67:549-559. [PMID: 29458679 DOI: 10.1099/jmm.0.000690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Crohn's disease is a chronic debilitating intestinal syndrome of unknown aetiology that is thought to result in part from an imbalance (dysbiosis) of the intestinal microbial populations, known as the microbiota. In this study we sought to compare the microbiota at the mucosal and submucosal levels at the resection margin in Crohn's disease to those in other intestinal dysbiotic disease controls to determine the level of bacterial translocation. METHODOLOGY 16S microbiota sequencing was performed on DNA extracted from mucosal and submucosal samples from resected intestinal tissues from Crohn's disease and controls. RESULTS Grossly normal appearing tissue at the resection margin showed early signs, suggesting bacterial translocation, with two bacterial families having penetrated the mucosal surfaces. In contrast, 4 and 13 bacterial families were present within submucosal tissues at the disease centre and disease margin, respectively. Although there was no significant difference in biodiversity, there was increased bacterial richness in the Crohn's disease group as compared to non-IBD controls. CONCLUSION The presence and/or absence of certain bacteria suggested disease-specific ecological or micro-environmental pressures driving or excluding certain organisms in Crohn's disease. The data suggest that several of the dysbiotic conditions previously reported for Crohn's disease are not unique but common to general dysbiosis. The examination of multiple intestinal sites in advanced disease may provide a spectrum of disease from early onset at the resection margin to active disease at the disease margin and late-stage fibrostenotic disease at the centre of the lesion, and a unique etiopathogenic view of Crohn's disease.
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Affiliation(s)
- Rodrick J Chiodini
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA.,St Vincent Healthcare, Sisters of Charity of Leavenworth Health System, Billings, MT, USA
| | - Scot E Dowd
- Molecular Research (Mr DNA), Shallowater, TX, USA
| | - James N Barron
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA
| | - Susan Galandiuk
- Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Brian Davis
- Department of Surgery, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Angela Glassing
- Department of Biological and Physical Sciences, Montana State University-Billings, Billings, MT, USA
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33
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Henson MA, Phalak P. Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis. BMC SYSTEMS BIOLOGY 2017; 11:145. [PMID: 29282051 PMCID: PMC5745886 DOI: 10.1186/s12918-017-0522-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn's disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli. One hypothesis is that chronic inflammation induces increased oxygen levels in the gut, which in turn causes an imbalance between obligate and facultative anaerobes. RESULTS To computationally investigate the oxygen hypothesis, we developed a multispecies biofilm model based on genome-scale metabolic reconstructions of F. prausnitzii, E. coli and the common gut anaerobe Bacteroides thetaiotaomicron. Application of low bulk oxygen concentrations at the biofilm boundary reproduced experimentally observed behavior characterized by a sharp decrease of F. prausnitzii and a large increase of E. coli, demonstrating that dysbiosis consistent with IBD disease progression could be qualitatively predicted solely based on metabolic differences between the species. A diet with balanced carbohydrate and protein content was predicted to represent a metabolic "sweet spot" that increased the oxygen range over which F. prausnitzii could remain competitive and IBD could be sublimated. Host-microbiota feedback incorporated via a simple linear feedback between the average F. prausnitzii concentration and the bulk oxygen concentration did not substantially change the range of oxygen concentrations where dysbiosis was predicted, but the transition from normal species abundances to severe dysbiosis was much more dramatic and occurred over a much longer timescale. Similar predictions were obtained with sustained antibiotic treatment replacing a sustained oxygen perturbation, demonstrating how IBD might progress over several years with few noticeable effects and then suddenly produce severe disease symptoms. CONCLUSIONS The multispecies biofilm metabolic model predicted that oxygen concentrations of ∼1 micromolar within the gut could cause microbiota dysbiosis consistent with those observed experimentally for inflammatory bowel diseases. Our model predictions could be tested directly through the development of an appropriate in vitro system of the three species community and testing of microbiota-host interactions in gnotobiotic mice.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and the Institute for Applied Life Sciences, University of Massachusetts, 140 Thatcher Way, Amherst, 01003 MA USA
| | - Poonam Phalak
- Department of Chemical Engineering and the Institute for Applied Life Sciences, University of Massachusetts, 140 Thatcher Way, Amherst, 01003 MA USA
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34
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Sipos F, Székely H, Kis ID, Tulassay Z, Műzes G. Relation of the IGF/IGF1R system to autophagy in colitis and colorectal cancer. World J Gastroenterol 2017; 23:8109-8119. [PMID: 29290648 PMCID: PMC5739918 DOI: 10.3748/wjg.v23.i46.8109] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 10/28/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023] Open
Abstract
Metabolic syndrome (MetS), as a chronic inflammatory disorder has a potential role in the development of inflammatory and cancerous complications of the colonic tissue. The interaction of DNA damage and inflammation is affected by the insulin-like growth factor 1 receptor (IGF1R) signaling pathway. The IGF1R pathway has been reported to regulate autophagy, as well, but sometimes through a bidirectional context. Targeting the IGF1R-autophagy crosstalk could represent a promising strategy for the development of new antiinflammatory and anticancer therapies, and may help for subjects suffering from MetS who are at increased risk of colorectal cancer. However, therapeutic responses to targeted therapies are often shortlived, since a signaling crosstalk of IGF1R with other receptor tyrosine kinases or autophagy exists, leading to acquired cellular resistance to therapy. From a pharmacological point of view, it is attractive to speculate that synergistic benefits could be achieved by inhibition of one of the key effectors of the IGF1R pathway, in parallel with the pharmacological stimulation of the autophagy machinery, but cautiousness is also required, because pharmacologic IGF1R modulation can initiate additional, sometimes unfavorable biologic effects.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest 1088, Hungary
| | - Hajnal Székely
- 2nd Department of Internal Medicine, Semmelweis University, Budapest 1088, Hungary
| | - Imre Dániel Kis
- Faculty of Medicine, Semmelweis University, Budapest 1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest 1088, Hungary
| | - Györgyi Műzes
- 2nd Department of Internal Medicine, Semmelweis University, Budapest 1088, Hungary
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35
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Lerner A, Matthias T, Aminov R. Potential Effects of Horizontal Gene Exchange in the Human Gut. Front Immunol 2017; 8:1630. [PMID: 29230215 PMCID: PMC5711824 DOI: 10.3389/fimmu.2017.01630] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/09/2017] [Indexed: 01/02/2023] Open
Abstract
Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host-microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically respond including lifestyle, therapy, diet, refined food, food additives, consumption of pre- and probiotics, and many others. The impact of the changing selective pressures on gut microbiota, however, is poorly understood. Presumably, the gut microbiome responds to these changes by genetic restructuring of gut populations, driven mainly via horizontal gene exchange. Thus, our main goal is to reveal the role played by horizontal gene exchange in the changing landscape of the gastrointestinal microbiome and potential effect of these changes on human health in general and autoimmune diseases in particular.
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Affiliation(s)
- Aaron Lerner
- B. Rappaport School of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,AESKU.KIPP Institute, Wendelsheim, Germany
| | | | - Rustam Aminov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,School of Medicine & Dentistry, University of Aberdeen, Aberdeen, United Kingdom
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Shwaartz C, Fields AC, Sobrero M, Divino CM. Does bowel preparation for inflammatory bowel disease surgery matter? Colorectal Dis 2017; 19:832-839. [PMID: 28436176 DOI: 10.1111/codi.13693] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022]
Abstract
AIM The purpose of this study was to determine if bowel preparation influences outcomes in patients with inflammatory bowel disease undergoing surgery. METHODS The database of the American College of Surgeons National Surgical Quality Improvement Program, Procedure Targeted Colectomy, from 2012 to 2014 was analyzed. Inflammatory bowel disease patients undergoing colorectal resection with or without bowel preparation were included in the study. RESULTS In all, 3679 patients with inflammatory bowel disease were identified. 42.5% had no bowel preparation, 21.5% had mechanical bowel preparation only, 8.8% had oral antibiotic bowel preparation only and 27.2% had combined mechanical and oral antibiotic preparation. Combined mechanical and oral antibiotic preparation is associated with lower rates of anastomotic leak, ileus, surgical site infection, organ space infection, wound dehiscence and sepsis/septic shock. CONCLUSION Combined mechanical and oral antibiotic preparation for inflammatory bowel disease patients undergoing colectomy is associated with decreased rates of surgical site infection, anastomotic leak, ileus. Combined bowel preparation should be the standard of care for inflammatory bowel disease patients undergoing colorectal resection.
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Affiliation(s)
- C Shwaartz
- Department of Surgery, Division of General Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - A C Fields
- Department of Surgery, Division of General Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - M Sobrero
- Department of Surgery, Division of General Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - C M Divino
- Department of Surgery, Division of General Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Host Genetics and Gut Microbiome: Challenges and Perspectives. Trends Immunol 2017; 38:633-647. [PMID: 28669638 DOI: 10.1016/j.it.2017.06.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/02/2017] [Accepted: 06/07/2017] [Indexed: 02/06/2023]
Abstract
The mammalian gut is colonized by trillions of microorganisms collectively called the microbiome. It is increasingly clear that this microbiome has a critical role of in many aspects of health including metabolism and immunity. While environmental factors such as diet and medications have been shown to influence the microbiome composition, the role of host genetics has only recently emerged in human studies and animal models. In this review, we summarize the current state of microbiome research with an emphasis on the effect of host genetics on the gut microbiome composition. We focus particularly on genetic determinants of the host immune system that help shape the gut microbiome and discuss avenues for future research.
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38
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Pierzchalska M, Panek M, Czyrnek M, Gielicz A, Mickowska B, Grabacka M. Probiotic Lactobacillus acidophilus bacteria or synthetic TLR2 agonist boost the growth of chicken embryo intestinal organoids in cultures comprising epithelial cells and myofibroblasts. Comp Immunol Microbiol Infect Dis 2017; 53:7-18. [PMID: 28750869 DOI: 10.1016/j.cimid.2017.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 05/31/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023]
Abstract
The intestinal epithelial cells reside in close proximity to myofibroblasts and microbiota, which are supposed to have an impact on intestinal stem cells fate and to influence processes of tissue maturation and regeneration. Mechanism underlying these phenomena and their diversity among vertebrates can be studied in 3D organoid cultures. We investigated the growth of chicken embryo intestinal epithelial organoids in Matrigel with and without Toll-like receptors (TLRs) stimulation. The organoid cultures contained also some myofibroblasts with potential to promote intestinal stem cell survival. Organoid cells, expressing TLR4, TLR2 type 1 and TLR2 type 2 were incubated with their agonists (lipopolysaccharide - LPS and Pam3CSK4) or co-cultured with Lactobacillus acidophilus bacteria (LA-5). Pam3CSK4 and LA-5 promoted organoid growth, which was demonstrated by comparing the morphological parameters (mean number and area of organoids). The profile of prostaglandins (PG), known to promote intestinal regeneration, in supernatants from organoid and fibroblast cultures were evaluated. Both PGE2 and PGD2 were detected. As compared to unstimulated controls, supernatants from the Pam3CSK4-stimulated organoids contained twice as much of PGE2 and PGD2. The changes in production of prostaglandins and the support of epithelial cell growth by myofibroblasts are factors potentially responsible for stimulatory effect of TLR2 activation.
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Affiliation(s)
- Malgorzata Pierzchalska
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland.
| | - Malgorzata Panek
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Malgorzata Czyrnek
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Anna Gielicz
- Department of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Barbara Mickowska
- Malopolska Center of Food Monitoring, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
| | - Maja Grabacka
- Department of Food Biotechnology, Faculty of Food Technology, The University of Agriculture in Kraków, Balicka 122, 30-149, Kraków, Poland
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Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, Nagarkatti M. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur J Immunol 2017; 47:1188-1199. [PMID: 28543188 DOI: 10.1002/eji.201646792] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/17/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023]
Abstract
Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of EAE, a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short-chain fatty acid (SCFA) production in CD44 knockout (CD44KO) mice. Fecal transfer from naïve CD44KO but not C57BL/6 wild type (CD44WT) mice, into EAE-induced CD44WT mice, led to significant amelioration of EAE. High-throughput bacterial 16S rRNA gene sequencing, followed by clustering sequences into operational taxonomic units (OTUs) and biochemical analysis, revealed that EAE-induced CD44KO mice showed significant diversity, richness, and evenness when compared to EAE-induced CD44WT mice at the phylum level, with dominant Bacteroidetes (68.5%) and low Firmicutes (26.8%). Further, data showed a significant change in the abundance of SCFAs, propionic acid, and i-butyric acid in EAE-CD44KO compared to EAE-CD44WT mice. In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs. Furthermore, our studies also demonstrate that the phenotype of gene knock-out animals may be shaped by gut microbiota.
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Affiliation(s)
| | - Hongbing Guan
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA.,Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Narendra P Singh
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Brandon Busbee
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Alexa Gandy
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Pegah Mehrpouya-Bahrami
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Mitra S Ganewatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Chuanbing Tang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Saurabh Chatterjee
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA.,WJB Dorn VA Medical Center, Columbia, SC, USA
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Wang JZ, Du WT, Xu YL, Cheng SZ, Liu ZJ. Gut microbiome-based medical methodologies for early-stage disease prevention. Microb Pathog 2017; 105:122-130. [DOI: 10.1016/j.micpath.2017.02.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/14/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
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41
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Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome. Processes (Basel) 2017. [DOI: 10.3390/pr5010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Abstract
Nucleotide-binding oligomerization domain 2 (NOD2) is an intracellular pattern recognition receptor that senses bacterial peptidoglycan (PGN)-conserved motifs in cytosol and stimulates host immune response. The association of NOD2 mutations with a number of inflammatory pathologies, including Crohn disease (CD), Graft-versus-host disease (GVHD), and Blau syndrome, highlights its pivotal role in host–pathogen interactions and inflammatory response. Stimulation of NOD2 by its ligand (muramyl dipeptide) activates pro-inflammatory pathways such as nuclear factor-κB (NF-κB), mitogen-activated protein kinases (MAPKs), and Caspase-1. A loss of NOD2 function may result in a failure in the control of microbial infection, thereby initiating systemic responses and aberrant inflammation. Because the ligand of Nod2 is conserved in both gram-positive and gram-negative bacteria, NOD2 detects a wide variety of microorganisms. Furthermore, current literature evidences that NOD2 is also able to control viruses’ and parasites’ infections. In this review, we present and discuss recent developments about the role of NOD2 in shaping the gut commensal microbiota and pathogens, including bacteria, viruses, and parasites, and the mechanisms by which Nod2 mutations participate in disease occurrence.
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Affiliation(s)
- Ziad Al Nabhani
- Laboratoire Inflamex, Université Paris-Diderot Sorbonne Paris-Cité, Paris, France
- INSERM, UMR 1149, Paris, France
| | - Gilles Dietrich
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Jean-Pierre Hugot
- Laboratoire Inflamex, Université Paris-Diderot Sorbonne Paris-Cité, Paris, France
- INSERM, UMR 1149, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Robert Debré, Paris, France
- * E-mail: (JPH); (FB)
| | - Frederick Barreau
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
- * E-mail: (JPH); (FB)
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The Interplay between Defensins and Microbiota in Crohn's Disease. Mediators Inflamm 2017; 2017:8392523. [PMID: 28246439 PMCID: PMC5299173 DOI: 10.1155/2017/8392523] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/16/2016] [Accepted: 01/04/2017] [Indexed: 02/08/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammation of the intestinal mucosa, characterized by periods of acute recurrence and remission. Depending on the specific region affected, CD is classified as ileal CD or colonic CD. It is largely accepted that the intestinal microbiota is involved in the onset of the pathology. Indeed, a reduced immune tolerance to components of the intestinal commensal microbiota and inflammation of the intestinal barrier typifies patients with CD. Several studies have shown defective expression of intestinal antimicrobial peptides (AMPs) in patients with CD compared to controls, particularly defensins. A reduction in α-defensins is observed in ileal CD, while β-defensins are increased in colonic CD. In addition to an immunological basis, the disease is frequently associated with genetic alterations including mutations of NOD2 gene. Several therapeutic strategies to circumvent the dysfunction observed in CD are currently under investigation. These include the use of delivery systems to administer endogenous AMPs and the engineering of peptidomimetics that could ameliorate the severity of CD. In this review, the role defensins play in CD and the strategies aimed at overcoming bacterial resistance will be discussed.
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Furfaro F, Gilardi D, Allocca M, Cicerone C, Correale C, Fiorino G, Danese S. IL-23 Blockade for Crohn s disease: next generation of anti-cytokine therapy. Expert Rev Clin Immunol 2017; 13:457-467. [PMID: 28067059 DOI: 10.1080/1744666x.2017.1279055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Adaptive immunity in intestinal inflammation may play a key role in the pathogenesis of Crohn's disease. In particular, interleukin (IL)-23 may be a key mediator in chronic intestinal inflammation by inducing the differentiation of naïve CD4 + T cells into Th17, with the production of several pro-inflammatory cytokines. Furthermore, IL-23 induces interferon-γ (IFN- γ) production from activated T cells, a critical cytokine in innate and adaptive immunity against infections. Areas covered: We aim to review the available data from literature regarding the role of IL-23, with a more specific focus on the recent progresses in the therapeutic modulation of this cytokine. Expert commentary: Increased knowledge regarding the role of IL-23 has allowed for the development of effective therapeutic progresses by blocking the IL-23 mediated pathways. Primary or secondary loss of response to anti-TNF therapies in Crohn's disease patients during the first year is widely described in literature: the development of new drugs, with alternative mechanisms of action, is thus a key point to consider for the optimal management of these subjects. Drugs blocking the IL-12/23 pathway showed a good efficacy and safety profile in immune-mediated diseases Further studies are necessary regarding the role of the single blockade of IL-23.
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Affiliation(s)
- Federica Furfaro
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy
| | - Daniela Gilardi
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy
| | - Mariangela Allocca
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy
| | - Clelia Cicerone
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy.,b Department of Internal Medicine and Medical Specialties , Sapienza University , Rome , Italy
| | - Carmen Correale
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy
| | - Gionata Fiorino
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy
| | - Silvio Danese
- a IBD Center, Department of Gastroenterology , Humanitas Research Hospital , Rozzano , Milan , Italy.,c Department of Biomedical Sciences , Humanitas University , Rozzano , Milan , Italy
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Alhagamhmad MH, Day AS, Lemberg DA, Leach ST. An overview of the bacterial contribution to Crohn disease pathogenesis. J Med Microbiol 2016; 65:1049-1059. [PMID: 27501828 DOI: 10.1099/jmm.0.000331] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Crohn disease (CD) is a chronic inflammatory condition primarily affecting the gastro-intestinal tract and is characterized by reduced bacterial diversity. The exact cause of disease is unknown; however, evidence suggests that several components, including microbiota, may contribute to the underlying pathology and disease development. Perturbation of the host-microbe commensal relationship is considered the main driving force of tissue destruction and pathological changes seen in CD. Several putative bacterial pathogens including species from Mycobacterium, Campylobacter and Helicobacter are postulated in the aetiology of CD. However, to date, no strong evidence supports a single bacterium contributing overall to CD pathogenesis. Alternatively, dysbiosis or bacterial imbalance is more widely accepted as a leading factor in the disrupted host-immune system cross-talk resulting in subsequent intestinal inflammation. Depletion of symbiont microbes including Firmicutes, Bifidobacterium and Clostridia, in conjunction with an increase in pathobiont microbes from Bacteroidetes and Enterobacteria, is a striking feature observed in CD. No single factor has been identified as driving this dysbiosis, although diet, antibiotic exposure and possible early life events in presence of underlying genetic susceptibility may contribute. The aim of this review is to highlight the current accumulating literature on the proposed role of bacteria in the pathogenesis of CD.
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Affiliation(s)
- Moftah H Alhagamhmad
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Andrew S Day
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
| | - Daniel A Lemberg
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Department of Gastroenterology, Sydney Children's Hospital, Randwick, Sydney, NSW, Australia
| | - Steven T Leach
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
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