101
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Are Faecal Microbiota Analyses on Species-Level Suitable Clinical Biomarkers? A Pilot Study in Subjects with Morbid Obesity. Microorganisms 2021; 9:microorganisms9030664. [PMID: 33806783 PMCID: PMC8005088 DOI: 10.3390/microorganisms9030664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND An abnormal faecal microbiota could be a causal factor for disease. This study evaluated a new method for faecal microbiota analysis in subjects with obesity and irritable bowel syndrome. METHODS The study had a matched case-control design. Forty-six subjects with morbid obesity (defined as BMI > 40 or >35 kg/m2 with obesity-related complications) of whom 23 had irritable bowel syndrome (IBS), were compared with 46 healthy volunteers. The faecal microbiota was analysed with Precision Microbiome Profiling (PMP™) which quantified 104 bacteria species. The primary aim was comparisons between the cases and controls. RESULTS Two men and 44 women with a mean age of 43.6 years were included in each of the groups; BMI in the groups was (mean and SD) 41.9 (3.5) and 22.5 (1.5) kg/m2, respectively. Seventeen bacterial species showed statistically significant differences between the groups after adjusting for multiple testing. In a post hoc analysis, the sensitivity and specificity were 78%. Alpha diversity was lower in the group with obesity. In subjects with morbid obesity, no clinically significant differences were seen between subjects with and without IBS or from before to six months after bariatric surgery. CONCLUSIONS The results encourage further evaluation of the new microbiome profiling tool.
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102
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Corley DA, Peek RM, Simpson BA. Paradigm-Shifting Research in Gastroenterology, Hepatology, and Nutrition: A Top 20 List of Articles Published in 2020. Gastroenterology 2021; 160:979-981. [PMID: 33548197 DOI: 10.1053/j.gastro.2021.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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103
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Zhao X, Liu H, Zhou X, Chen X, Hu N, Zhang Y, Wang S. 2-Amino-1-methyl-6-phenylimidazo[4,5- b]pyridine Induced Colon Injury by Disrupting the Intestinal Bacterial Composition and Lipid Metabolic Pathways in Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:437-446. [PMID: 33373210 DOI: 10.1021/acs.jafc.0c06588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), one of the most abundant heterocyclic amines, is a common carcinogen produced in thermally processed protein-rich foods. Studies have demonstrated that PhIP could induce colon tumors in rodents, leaving mechanisms uncovered. This study aims to investigate the mechanism of PhIP-induced colon injury in a rat model. The results of 16S rRNA gene sequencing and metabolomics showed that PhIP disrupted intestinal bacterial composition and affected the glycerophospholipid metabolism and linoleic acid metabolism. Simultaneously, the lipid metabolism function in the intestinal flora was inhibited by PhIP. Notably, transcriptomics revealed that PhIP remarkably inhibited the expression of gene sets associated with steroid hormone biosynthesis, fatty acid elongation, fatty acid degradation, and glycerolipid metabolism pathways in the colon. The results provide new perspectives to study the mechanism of PhIP-induced colon injury and theoretical bases for further understanding the toxicity of PhIP.
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Affiliation(s)
- Xiuli Zhao
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Hengchao Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xiaofei Zhou
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Xiaoxu Chen
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Nan Hu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Yan Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, People's Republic of China
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104
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Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components. J Pers Med 2021; 11:jpm11010035. [PMID: 33429936 PMCID: PMC7827153 DOI: 10.3390/jpm11010035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023] Open
Abstract
The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.
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105
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The fecal mycobiome in patients with Irritable Bowel Syndrome. Sci Rep 2021; 11:124. [PMID: 33420127 PMCID: PMC7794320 DOI: 10.1038/s41598-020-79478-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Alterations of the gut microbiota have been reported in various gastrointestinal disorders, but knowledge of the mycobiome is limited. We investigated the gut mycobiome of 80 patients with Irritable Bowel Syndrome (IBS) in comparison with 64 control subjects. The fungal-specific internal transcribed spacer 1 (ITS-1) amplicon was sequenced, and mycobiome zero-radius operational taxonomic units (zOTUs) were defined representing known and unknown species and strains. The fungal community was sparse and individual-specific in all (both IBS and control) subjects. Although beta-diversity differed significantly between IBS and controls, no difference was found among clinical subtypes of IBS or in comparison with the mycobiome of subjects with bile acid malabsorption (BAM), a condition which may overlap with IBS with diarrhoea. The mycobiome alterations co-varied significantly with the bacteriome and metabolome but were not linked with dietary habits. As a putative biomarker of IBS, the predictive power of the fecal mycobiome in machine learning models was significantly better than random but insufficient for clinical diagnosis. The mycobiome presents limited therapeutic and diagnostic potential for IBS, despite co-variation with bacterial components which do offer such potential.
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106
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Kamp KJ, Cain KC, Utleg A, Burr RL, Raftery D, Luna RA, Shulman RJ, Heitkemper MM. Bile Acids and Microbiome Among Individuals With Irritable Bowel Syndrome and Healthy Volunteers. Biol Res Nurs 2021; 23:65-74. [PMID: 32666807 PMCID: PMC7874368 DOI: 10.1177/1099800420941255] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. High bile acid (BA) profiles have been associated with abdominal pain symptoms, mucosal inflammation, and diarrhea in a subgroup of those with IBS. The purpose of this study was to compare: 1) fecal primary and secondary BAs in women with and without IBS; and 2) symptoms, gut microbiome, and diet between women with high and normal BAs (i.e., similar to healthy [HC] women). Women (ages 18-45) with IBS and HCs were recruited from healthcare providers or the community. Participants kept a 28-day symptom diary, completed a 3-day food journal, and collected a stool sample for microbiome analysis (16 S rRNA gene sequencing). Primary and secondary BA levels were determined by mass spectrometry. Primary BAs did not differ between IBS (n = 45) and HC (n = 28) groups; women with IBS had significantly increased conjugated secondary BAs (glycodeoxycholic acid [p = 0.006], taurodeoxycholic acid [p = 0.006], and glycolithocholic acid [p = 0.01]). Sixty percent of women with IBS had normal BAs whereas 40% had high BAs. Women with high fecal BAs were predominantly IBS-Diarrhea or IBS-Mixed and consumed less fiber and vegetable protein and more animal protein compared to women with IBS whose fecal BAs levels were comparable to HCs. Those with high conjugated secondary fecal BAs also had a greater Firmicutes/Bacteroidetes ratio, less abundance of phylum Bacteroidetes and genus Gemmiger, and more abundance of family Erysipelotrichaceae compared to IBS women with normal BAs. Determination of fecal BA levels provides additional insights into pathophysiological links between diet and microbiome in IBS.
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Affiliation(s)
- Kendra J Kamp
- Division of Gastroenterology, School of Medicine, 7284University of Washington, Seattle, WA, USA
| | - Kevin C Cain
- Department of Biostatistics, School of Public Health, 7284University of Washington, Seattle, WA, USA
| | - Angelita Utleg
- School of Nursing, 7284University of Washington, Seattle, WA, USA
| | - Robert L Burr
- Department of Biobehavioral Nursing and Health Informatics, School of Nursing, 7284University of Washington, Seattle, WA, USA
| | - Daniel Raftery
- Department of Anesthesiology & Pain Medicine, 7284University of Washington, Seattle, WA, USA
| | | | | | - Margaret M Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, School of Nursing, 7284University of Washington, Seattle, WA, USA
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107
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O'Toole PW, Shanahan F. Transplanting Microbes for Irritable Bowels or Irritated Microbes or Both? Gastroenterology 2021; 160:15-17. [PMID: 33075346 DOI: 10.1053/j.gastro.2020.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Paul W O'Toole
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland.
| | - Fergus Shanahan
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
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108
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Mars RAT, Frith M, Kashyap PC. Functional Gastrointestinal Disorders and the Microbiome-What Is the Best Strategy for Moving Microbiome-based Therapies for Functional Gastrointestinal Disorders into the Clinic? Gastroenterology 2021; 160:538-555. [PMID: 33253687 PMCID: PMC8575137 DOI: 10.1053/j.gastro.2020.10.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
There have been numerous human studies reporting associations between the intestinal microbiome and functional gastrointestinal disorders (FGIDs), and independently animal studies have explored microbiome-driven mechanisms underlying FGIDs. However, there is often a disconnect between human and animal studies, which hampers translation of microbiome findings to the clinic. Changes in the microbiota composition of patients with FGIDs are generally subtle, whereas changes in microbial function, reflected in the fecal metabolome, appear to be more precise indicators of disease subtype-specific mechanisms. Although we have made significant progress in characterizing the microbiome, to effectively translate microbiome science in a timely manner, we need concurrent and iterative longitudinal studies in humans and animals to determine the precise microbial functions that can be targeted to address specific pathophysiological processes in FGIDs. A systems approach integrating multiple data layers rather than evaluating individual data layers of symptoms, physiological changes, or -omics data in isolation will allow for validation of mechanistic insights from animal studies while also allowing new discovery. Patient stratification for clinical trials based on functional microbiome alterations and/or pathophysiological measurements may allow for more accurate determination of efficacy of individual microbiome-targeted interventions designed to correct an underlying abnormality. In this review, we outline current approaches and knowledge, and identify gaps, to provide a potential roadmap for accelerating translation of microbiome science toward microbiome-targeted personalized treatments for FGIDs.
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Affiliation(s)
- Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Mary Frith
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota.
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109
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Coughlan S, Das A, O’Herlihy E, Shanahan F, O’Toole P, Jeffery I. The gut virome in Irritable Bowel Syndrome differs from that of controls. Gut Microbes 2021; 13:1-15. [PMID: 33602058 PMCID: PMC7899630 DOI: 10.1080/19490976.2021.1887719] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/28/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.
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Affiliation(s)
- S. Coughlan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - A. Das
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - E. O’Herlihy
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - F. Shanahan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - P.W. O’Toole
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - I.B. Jeffery
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
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110
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Jeffery IB, O'Herlihy E, Shanahan F, O' Toole PW. Microbiome alterations in IBS. Gut 2020; 69:2263-2264. [PMID: 32139549 DOI: 10.1136/gutjnl-2020-320919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Fergus Shanahan
- 4D Pharma Cork Ltd, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W O' Toole
- 4D Pharma Cork Ltd, Cork, Ireland .,School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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111
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The pathophysiology of bile acid diarrhoea: differences in the colonic microbiome, metabolome and bile acids. Sci Rep 2020; 10:20436. [PMID: 33235223 PMCID: PMC7686486 DOI: 10.1038/s41598-020-77374-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Bile acid diarrhoea (BAD) is a common disorder resulting from increased loss of bile acids (BAs), overlapping irritable bowel syndrome with diarrhoea (IBS-D). The gut microbiota metabolises primary BAs to secondary BAs, with differing impacts on metabolism and homeostasis. The aim of this study was to profile the microbiome, metabolic products and bile acids in BAD. Patients with BAD diagnosed by SeHCAT testing, were compared with other IBS-D patients, and healthy controls. Faecal 16S ribosomal RNA gene analysis was undertaken. Faecal short chain fatty acid (SCFA) and urinary volatile organic compounds (VOCs) were measured. BAs were quantified in serum and faeces. Faecal bacterial diversity was significantly reduced in patients with BAD. Several taxa were enriched compared to IBS-D. SCFA amounts differed in BAD, controls and IBS-D, with significantly more propionate in BAD. Separation of VOC profiles was evident, but the greatest discrimination was between IBS-D and controls. Unconjugated and primary BA in serum and faeces were significantly higher in BAD. The faecal percentage primary BA was inversely related to SeHCAT. BAD produces dysbiosis, with metabolite differences, including VOC, SCFA and primary BAs when compared to IBS-D. These findings provide new mechanistic insights into the pathophysiology of BAD.
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112
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Ford AC, Sperber AD, Corsetti M, Camilleri M. Irritable bowel syndrome. Lancet 2020; 396:1675-1688. [PMID: 33049223 DOI: 10.1016/s0140-6736(20)31548-8] [Citation(s) in RCA: 347] [Impact Index Per Article: 86.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/26/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022]
Abstract
Irritable bowel syndrome is a functional gastrointestinal disorder with symptoms including abdominal pain associated with a change in stool form or frequency. The condition affects between 5% and 10% of otherwise healthy individuals at any one point in time and, in most people, runs a relapsing and remitting course. The best described risk factor is acute enteric infection, but irritable bowel syndrome is also more common in people with psychological comorbidity and in young adult women than in the rest of the general population. The pathophysiology of irritable bowel syndrome is incompletely understood, but it is well established that there is disordered communication between the gut and the brain, leading to motility disturbances, visceral hypersensitivity, and altered CNS processing. Other less reproducible mechanisms might include genetic associations, alterations in gastrointestinal microbiota, and disturbances in mucosal and immune function. In most people, diagnosis can be made on the basis of clinical history with limited and judicious use of investigations, unless alarm symptoms such as weight loss or rectal bleeding are present, or there is a family history of inflammatory bowel disease or coeliac disease. Once the diagnosis is made, an empathetic approach is key and can improve quality of life and symptoms, and reduce health-care expenditure. The mainstays of treatment include patient education about the condition, dietary changes, soluble fibre, and antispasmodic drugs. Other treatments tend to be reserved for people with severe symptoms and include central neuromodulators, intestinal secretagogues, drugs acting on opioid or 5-HT receptors, or minimally absorbed antibiotics (all of which are selected according to predominant bowel habit), as well as psychological therapies. Increased understanding of the pathophysiology of irritable bowel syndrome in the past 10 years has led to a healthy pipeline of novel drugs in development.
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Affiliation(s)
- Alexander C Ford
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK; Leeds Gastroenterology Institute, St James's University Hospital, Leeds, UK.
| | - Ami D Sperber
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maura Corsetti
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Mayo Clinic, Rochester, MN, USA
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113
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Yang M, Hong G, Jin Y, Li Y, Li G, Hou X. Mucosal-Associated Microbiota Other Than Luminal Microbiota Has a Close Relationship With Diarrhea-Predominant Irritable Bowel Syndrome. Front Cell Infect Microbiol 2020; 10:515614. [PMID: 33224895 PMCID: PMC7667041 DOI: 10.3389/fcimb.2020.515614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Studies have linked dysbiosis of gut microbiota to irritable bowel syndrome (IBS). However, dysbiosis only referring to structural changes without functional alteration or focusing on luminal microbiota are incomplete. To fully investigate the relationship between gut microbiota and clinical symptoms of Irritable Bowel Syndrome with Diarrhea (IBS-D), fecal samples, and rectal mucosal biopsies were collected from 69 IBS-D patients and 20 healthy controls (HCs) before and during endoscopy without bowel preparation. 16S rRNA genes were amplified and sequenced, and QIIME pipeline was used to process the composition of microbial communities. PICRUSt was used to predict and categorize microbial function. The composition of mucosa-associated microbiota (MAM) was significantly different in IBS-D patients compared to HCs; while no difference in luminal microbiota (LM). MAM, but not LM, was significantly positively correlated with abdominal pain and bloating. A greater number of MAM functional genes changed in IBS-D patients than that of LM compared with HCs. Metabolic alteration in MAM not in LM was related to abdominal pain and bloating. There was a close relationship between the composition and function of MAM and clinical symptoms in IBS-D patients which suggests the important role of MAM in pathogenesis and therapies in IBS-D and it should be highlighted in the future.
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Affiliation(s)
- Min Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gaichao Hong
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Jin
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gangping Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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114
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Pretorius L, Smith C. The trace aminergic system: a gender-sensitive therapeutic target for IBS? J Biomed Sci 2020; 27:95. [PMID: 32981524 PMCID: PMC7520957 DOI: 10.1186/s12929-020-00688-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Due to a lack of specific or sensitive biomarkers, drug discovery advances have been limited for individuals suffering from irritable bowel syndrome (IBS). While current therapies provide symptomatic relief, inflammation itself is relatively neglected, despite the presence of chronic immune activation and innate immune system dysfunction. Moreover, considering the microgenderome concept, gender is a significant aetiological risk factor. We believe that we have pinpointed a "missing link" that connects gender, dysbiosis, diet, and inflammation in the context of IBS, which may be manipulated as therapeutic target. The trace aminergic system is conveniently positioned at the interface of the gut microbiome, dietary nutrients and by-products, and mucosal immunity. Almost all leukocyte populations express trace amine associated receptors and significant amounts of trace amines originate from both food and the gut microbiota. Additionally, although IBS-specific data are sparse, existing data supports an interpretation in favour of a gender dependence in trace aminergic signalling. As such, trace aminergic signalling may be altered by fluctuations of especially female reproductive hormones. Utilizing a multidisciplinary approach, this review discusses potential mechanisms of actions, which include hyperreactivity of the immune system and aberrant serotonin signalling, and links outcomes to the symptomology clinically prevalent in IBS. Taken together, it is feasible that the additional level of regulation by the trace aminergic system in IBS has been overlooked, until now. As such, we suggest that components of the trace aminergic system be considered targets for future therapeutic action, with the specific focus of reducing oxidative stress and inflammation.
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Affiliation(s)
- Lesha Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa
| | - Carine Smith
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa.
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115
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Farrugia A, Arasaradnam R. Bile acid diarrhoea: pathophysiology, diagnosis and management. Frontline Gastroenterol 2020; 12:500-507. [PMID: 34712468 PMCID: PMC8515273 DOI: 10.1136/flgastro-2020-101436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 02/04/2023] Open
Abstract
The actual incidence of bile acid diarrhoea (BAD) is unknown, however, there is increasing evidence that it is misdiagnosed in up to 30% with diarrhoea-predominant patients with irritable bowel syndrome. Besides this, it may also occur following cholecystectomy, infectious diarrhoea and pelvic chemoradiotherapy. BAD may result from either hepatic overproduction of bile acids or their malabsorption in the terminal ileum. It can result in symptoms such as bowel frequency, urgency, nocturnal defecation, excessive flatulence, abdominal pain and incontinence of stool. Bile acid synthesis is regulated by negative feedback loops related to the enterohepatic circulation, which are dependent on the farnesoid X receptor and fibroblast growth factor 19. Interruption of these feedback loops is thought to cause bile acid overproduction leading to BAD. This process may occur idiopathically or following a specific trigger such as cholecystectomy. There may also be an interplay with the gut microbiota, which has been reported to be significantly different in patients with severe BAD. Patients with suspected BAD are investigated in various ways including radionucleotide imaging such as SeHCAT scans (though this is not available worldwide) and blood tests. However, other methods such as bile acid measurement in stool (either spot test or 48 hours samples) and urine tests have been explored. Importantly, delay in diagnosis and treatment of BAD greatly affects patient's quality of life and may double the overall cost of diagnosis.
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Affiliation(s)
- Alexia Farrugia
- Surgery, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK,Divison of Biomedical Sciences, University of Warwick, Warwick Medical School, Coventry, Coventry, UK
| | - Ramesh Arasaradnam
- Divison of Biomedical Sciences, University of Warwick, Warwick Medical School, Coventry, Coventry, UK,Gastroenterology, University Hospitals of Coventry and Warwickshire NHS Trust, Coventry, UK
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116
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Gallardo P, Izquierdo M, Vidal RM, Soto F, Ossa JC, Farfan MJ. Gut Microbiota-Metabolome Changes in Children With Diarrhea by Diarrheagenic E. coli. Front Cell Infect Microbiol 2020; 10:485. [PMID: 33072619 PMCID: PMC7531578 DOI: 10.3389/fcimb.2020.00485] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Diarrheagenic Escherichia coli (DEC) strains are a main cause of diarrhea worldwide in children under 5 years old. DEC virulence is strongly regulated by environmental conditions and metabolites produced by the gut microbiota in the intestinal tract. In this study, we evaluated changes in gut microbiota-metabolome in children with or without diarrhea produced by DEC pathotypes. Goal: To determine gut microbiota composition and metabolome in stool samples obtained from healthy children and children with diarrhea positive for DEC pathotypes. Methods: We analyzed a total of 16 age-paired stool samples: 8 diarrheal samples positive for one DEC pathotype and 8 stool samples from healthy children. To identify the microbiota composition, we sequenced the V3-V4 region of the 16S rRNA and determined operational phylogenetic units (OPU). OPU were then used to predict metabolic pathways using the PICRUSt2 software. The presence of metabolites in stool samples was determined by LC-MS. A correlation analysis was performed with the main genera from each group and main metabolites. Bacteria associated with variance of main metabolites were identified using the MIMOSA2 software. Results: DEC and healthy groups showed a statistically different microbiota composition. A decrease in Firmicutes together with an increase in Bacteroidetes and Proteobacteria was found in the DEC group compared to the healthy group. Metabolic pathway predictions based on microbiota diversity showed that pathways involved in histidine and L-ornithine metabolism were significantly different between groups. A total of 88 metabolites detected by LC-MS were included in the metabolome analysis. We found higher levels of histamine and lower levels of ornithine in DEC samples than in the healthy group. Histamine and L-ornithine were associated with a specific microbiota species and the corresponding metabolic pathways. Conclusion: Stool samples from healthy children and children positive for DEC displayed a differential metabolome and microbiota composition. A strong correlation between a gut microbiota species and certain metabolites, such as histamine and L-ornithine, was found in the DEC group. This information might be useful to identify mechanisms and signaling molecules involved in the crosstalk between microbiota and DEC pathotypes.
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Affiliation(s)
- Pablo Gallardo
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | - Mariana Izquierdo
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | - Roberto M Vidal
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Francisco Soto
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | - Juan C Ossa
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | - Mauricio J Farfan
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
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117
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Carco C, Young W, Gearry RB, Talley NJ, McNabb WC, Roy NC. Increasing Evidence That Irritable Bowel Syndrome and Functional Gastrointestinal Disorders Have a Microbial Pathogenesis. Front Cell Infect Microbiol 2020; 10:468. [PMID: 33014892 PMCID: PMC7509092 DOI: 10.3389/fcimb.2020.00468] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal tract harbors most of the microbial cells inhabiting the body, collectively known as the microbiota. These microbes have several implications for the maintenance of structural integrity of the gastrointestinal mucosal barrier, immunomodulation, metabolism of nutrients, and protection against pathogens. Dysfunctions in these mechanisms are linked to a range of conditions in the gastrointestinal tract, including functional gastrointestinal disorders, ranging from irritable bowel syndrome, to functional constipation and functional diarrhea. Irritable bowel syndrome is characterized by chronic abdominal pain with changes in bowel habit in the absence of morphological changes. Despite the high prevalence of irritable bowel syndrome in the global population, the mechanisms responsible for this condition are poorly understood. Although alterations in the gastrointestinal microbiota, low-grade inflammation and immune activation have been implicated in the pathophysiology of functional gastrointestinal disorders, there is inconsistency between studies and a lack of consensus on what the exact role of the microbiota is, and how changes to it relate to these conditions. The complex interplay between host factors, such as microbial dysbiosis, immune activation, impaired epithelial barrier function and motility, and environmental factors, including diet, will be considered in this narrative review of the pathophysiology of functional gastrointestinal disorders.
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Affiliation(s)
- Caterina Carco
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,Food Nutrition and Health Team, AgResearch Grasslands, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Wayne Young
- Riddet Institute, Massey University, Palmerston North, New Zealand.,Food Nutrition and Health Team, AgResearch Grasslands, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Richard B Gearry
- The High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Nicholas J Talley
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Liggins Institute, University of Auckland, Auckland, New Zealand.,Department of Human Nutrition, University of Otago, Dunedin, New Zealand
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118
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Ephraim E, Cochrane CY, Jewell DE. Varying Protein Levels Influence Metabolomics and the Gut Microbiome in Healthy Adult Dogs. Toxins (Basel) 2020; 12:toxins12080517. [PMID: 32806674 PMCID: PMC7472411 DOI: 10.3390/toxins12080517] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
The optimal ranges of protein for healthy adult dogs are not known. This study evaluated the impact of long-term consumption of foods containing low, medium, and high levels of protein on serum, urine, and fecal metabolites, and gut microbiome in beagles. Following maintenance on a prefeed food for 14 days, dogs (15 neutered males, 15 spayed females, aged 2–9 years, mean initial weight 11.3 kg) consumed the low (18.99%, dry matter basis), medium (25.34%), or high (45.77%) protein foods, each for 90 days, in a William’s Latin Square Design sequence. In serum and/or urine, metabolites associated with inflammation (9,10-dihydroxyoctadecanoic acid (DiHOME)), 12,13-DiHOME) and kidney dysfunction (urea, 5-hydroxyindole sulfate, 7-hydroxyindole sulfate, p-cresol sulfate) increased with higher protein levels in food, while one-carbon pathway metabolites (betaine, dimethylglycine, sarcosine) decreased. Fecal pH increased with protein consumed, and levels of beneficial indoles and short-chain fatty acids decreased while branched-chain fatty acids increased. Beta diversity of the fecal microbiome was significantly different, with increased abundances of proteolytic bacteria with higher protein food. Feeding dogs a high amount of protein leads to a shift to proteolytic gut bacteria, higher fecal pH, and is associated with increased levels of metabolites linked with inflammation and kidney dysfunction.
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Affiliation(s)
- Eden Ephraim
- Pet Nutrition Center, Hill’s Pet Nutrition, Inc., Topeka, KS 66617, USA;
- Correspondence:
| | - Chun-Yen Cochrane
- Pet Nutrition Center, Hill’s Pet Nutrition, Inc., Topeka, KS 66617, USA;
| | - Dennis E. Jewell
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS 66506, USA;
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119
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Lahtinen P, Jalanka J, Hartikainen A, Mattila E, Hillilä M, Punkkinen J, Koskenpato J, Anttila VJ, Tillonen J, Satokari R, Arkkila P. Letter: faecal microbiota transplantation for irritable bowel syndrome. Authors' reply. Aliment Pharmacol Ther 2020; 52:557-558. [PMID: 32656839 DOI: 10.1111/apt.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Perttu Lahtinen
- Department of Gastroenterology, Päijät-Häme Central Hospital, Lahti, Finland.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonna Jalanka
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eero Mattila
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Markku Hillilä
- Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Gastroenterology, Helsinki University Hospital, Espoo, Finland
| | - Jari Punkkinen
- Department of Gastroenterology, Porvoo Hospital, Porvoo, Finland
| | - Jari Koskenpato
- Department of Gastroenterology, Aava Medical Centre, Helsinki, Finland
| | - Veli-Jukka Anttila
- Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Jyrki Tillonen
- Department of Gastroenterology, Päijät-Häme Central Hospital, Lahti, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Perttu Arkkila
- Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
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120
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Bennet SM, Keshteli AH, Bercik P, Madsen KL, Reed D, Vanner SJ. Application of metabolomics to the study of irritable bowel syndrome. Neurogastroenterol Motil 2020; 32:e13884. [PMID: 32426922 DOI: 10.1111/nmo.13884] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 12/20/2022]
Abstract
The pathophysiology of irritable bowel syndrome and the detection of biomarkers of specific mechanisms and/or predictors of therapeutic response remain elusive. This roadblock reflects, in large part, the complexity and heterogeneity of the disorder. Recently, there has been growing evidence of a dietary and/or microbiome interaction with the host that may trigger symptoms in a subset of patients. While a number of techniques are available to examine these potential interactions, "omic" approaches such as metabolomics are becoming more widely used. Metabolomics measures hundreds and potentially thousands of known and unknown small molecule chemicals (metabolites) to provide a unique look into mechanisms that underlie symptom generation and potential predictors of therapeutic response. In this issue of the journal, Lee et al use nuclear magnetic resonance (NMR) to demonstrate the value of this approach to study IBS. This review examines the use of metabolomics to better understand IBS, focusing on what has been learned to date, practical and technical considerations, its potential for future research and how the study by Lee et al have contributed to these concepts.
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Affiliation(s)
- Sean M Bennet
- GI Diseases Research Unit, Queen's University, Kingston General Hospital, Kingston, ON, Canada
| | | | - Premysl Bercik
- Department of Medicine, Farncombe Institute, McMaster University, ON, Canada
| | | | - David Reed
- GI Diseases Research Unit, Queen's University, Kingston General Hospital, Kingston, ON, Canada
| | - Stephen J Vanner
- GI Diseases Research Unit, Queen's University, Kingston General Hospital, Kingston, ON, Canada
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121
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Wang Y, Zhou Y, Xiao X, Zheng J, Zhou H. Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota. J Proteomics 2020; 219:103737. [DOI: 10.1016/j.jprot.2020.103737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
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