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Salla M, Guo J, Joshi H, Gordon M, Dooky H, Lai J, Capicio S, Armstrong H, Valcheva R, Dyck JRB, Thiesen A, Wine E, Dieleman LA, Baksh S. Novel Biomarkers for Inflammatory Bowel Disease and Colorectal Cancer: An Interplay between Metabolic Dysregulation and Excessive Inflammation. Int J Mol Sci 2023; 24:ijms24065967. [PMID: 36983040 PMCID: PMC10055751 DOI: 10.3390/ijms24065967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Persistent inflammation can trigger altered epigenetic, inflammatory, and bioenergetic states. Inflammatory bowel disease (IBD) is an idiopathic disease characterized by chronic inflammation of the gastrointestinal tract, with evidence of subsequent metabolic syndrome disorder. Studies have demonstrated that as many as 42% of patients with ulcerative colitis (UC) who are found to have high-grade dysplasia, either already had colorectal cancer (CRC) or develop it within a short time. The presence of low-grade dysplasia is also predictive of CRC. Many signaling pathways are shared among IBD and CRC, including cell survival, cell proliferation, angiogenesis, and inflammatory signaling pathways. Current IBD therapeutics target a small subset of molecular drivers of IBD, with many focused on the inflammatory aspect of the pathways. Thus, there is a great need to identify biomarkers of both IBD and CRC, that can be predictive of therapeutic efficacy, disease severity, and predisposition to CRC. In this study, we explored the changes in biomarkers specific for inflammatory, metabolic, and proliferative pathways, to help determine the relevance to both IBD and CRC. Our analysis demonstrated, for the first time in IBD, the loss of the tumor suppressor protein Ras associated family protein 1A (RASSF1A), via epigenetic changes, the hyperactivation of the obligate kinase of the NOD2 pathogen recognition receptor (receptor interacting protein kinase 2 [RIPK2]), the loss of activation of the metabolic kinase, AMP activated protein kinase (AMPKα1), and, lastly, the activation of the transcription factor and kinase Yes associated protein (YAP) kinase, that is involved in proliferation of cells. The expression and activation status of these four elements are mirrored in IBD, CRC, and IBD-CRC patients and, importantly, in matched blood and biopsy samples. The latter would suggest that biomarker analysis can be performed non-invasively, to understand IBD and CRC, without the need for invasive and costly endoscopic analysis. This study, for the first time, illustrates the need to understand IBD or CRC beyond an inflammatory perspective and the value of therapeutics directed to reset altered proliferative and metabolic states within the colon. The use of such therapeutics may truly drive patients into remission.
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Armstrong HK, Bording-Jorgensen M, Santer DM, Zhang Z, Valcheva R, Rieger AM, Sung-Ho Kim J, Dijk SI, Mahmood R, Ogungbola O, Jovel J, Moreau F, Gorman H, Dickner R, Jerasi J, Mander IK, Lafleur D, Cheng C, Petrova A, Jeanson TL, Mason A, Sergi CM, Levine A, Chadee K, Armstrong D, Rauscher S, Bernstein CN, Carroll MW, Huynh HQ, Walter J, Madsen KL, Dieleman LA, Wine E. Unfermented β-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients. Gastroenterology 2023; 164:228-240. [PMID: 36183751 DOI: 10.1053/j.gastro.2022.09.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel diseases (IBD) are affected by dietary factors, including nondigestible carbohydrates (fibers), which are fermented by colonic microbes. Fibers are overall beneficial, but not all fibers are alike, and some patients with IBD report intolerance to fiber consumption. Given reproducible evidence of reduced fiber-fermenting microbes in patients with IBD, we hypothesized that fibers remain intact in select patients with reduced fiber-fermenting microbes and can then bind host cell receptors, subsequently promoting gut inflammation. METHODS Colonic biopsies cultured ex vivo and cell lines in vitro were incubated with oligofructose (5 g/L), or fermentation supernatants (24-hour anaerobic fermentation) and immune responses (cytokine secretion [enzyme-linked immunosorbent assay/meso scale discovery] and expression [quantitative polymerase chain reaction]) were assessed. Influence of microbiota in mediating host response was examined and taxonomic classification of microbiota was conducted with Kraken2 and metabolic profiling by HUMAnN2, using R software. RESULTS Unfermented dietary β-fructan fibers induced proinflammatory cytokines in a subset of IBD intestinal biopsies cultured ex vivo, and immune cells (including peripheral blood mononuclear cells). Results were validated in an adult IBD randomized controlled trial examining β-fructan supplementation. The proinflammatory response to intact β-fructan required activation of the NLRP3 and TLR2 pathways. Fermentation of β-fructans by human gut whole microbiota cultures reduced the proinflammatory response, but only when microbes were collected from patients without IBD or patients with inactive IBD. Fiber-induced immune responses correlated with microbe functions, luminal metabolites, and dietary fiber avoidance. CONCLUSION Although fibers are typically beneficial in individuals with normal microbial fermentative potential, some dietary fibers have detrimental effects in select patients with active IBD who lack fermentative microbe activities. The study is publicly accessible at the U.S. National Institutes of Health database (clinicaltrials.gov identification number NCT02865707).
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Affiliation(s)
- Heather K Armstrong
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Michael Bording-Jorgensen
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Deanna M Santer
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Zhengxiao Zhang
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada; College of Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Rosica Valcheva
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Aja M Rieger
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Justin Sung-Ho Kim
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie I Dijk
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, University of Alberta, Edmonton, Alberta, Canada
| | - Ramsha Mahmood
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Olamide Ogungbola
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Juan Jovel
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada
| | - France Moreau
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - Hayley Gorman
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - Robyn Dickner
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Jerasi
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Inderdeep K Mander
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Dawson Lafleur
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Cheng
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Alexandra Petrova
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Terri-Lyn Jeanson
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew Mason
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Consolato M Sergi
- Anatomic Pathology Division, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Arie Levine
- Pediatric Gastroenterology Unit, Wolfson Medical Center, Tel-Aviv University, Holon, Israel
| | - Kris Chadee
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
| | - David Armstrong
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Charles N Bernstein
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Matthew W Carroll
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Hien Q Huynh
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Jens Walter
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
| | - Karen L Madsen
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Levinus A Dieleman
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Eytan Wine
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Alberta, Canada; Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, University of Alberta, Edmonton, Alberta, Canada.
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Rashed R, Valcheva R, Dieleman LA. Manipulation of Gut Microbiota as a Key Target for Crohn's Disease. Front Med (Lausanne) 2022; 9:887044. [PMID: 35783604 PMCID: PMC9244564 DOI: 10.3389/fmed.2022.887044] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) sub-type characterized by transmural chronic inflammation of the gastrointestinal tract. Research indicates a complex CD etiology involving genetic predisposition and immune dysregulation in response to environmental triggers. The chronic mucosal inflammation has been associated with a dysregulated state, or dysbiosis, of the gut microbiome (bacteria), mycobiome (fungi), virome (bacteriophages and viruses), and archeaome (archaea) further affecting the interkingdom syntrophic relationships and host metabolism. Microbiota dysbiosis in CD is largely described by an increase in facultative anaerobic pathobionts at the expense of strict anaerobic Firmicutes, such as Faecalibacterium prausnitzii. In the mycobiome, reduced fungal diversity and fungal-bacteria interactions, along with a significantly increased abundance of Candida spp. and a decrease in Saccharomyces cerevisiae are well documented. Virome analysis also indicates a significant decrease in phage diversity, but an overall increase in phages infecting bacterial groups associated with intestinal inflammation. Finally, an increase in methanogenic archaea such as Methanosphaera stadtmanae exhibits high immunogenic potential and is associated with CD etiology. Common anti-inflammatory medications used in CD management (amino-salicylates, immunomodulators, and biologics) could also directly or indirectly affect the gut microbiome in CD. Other medications often used concomitantly in IBD, such as antibiotics, antidepressants, oral contraceptives, opioids, and proton pump inhibitors, have shown to alter the gut microbiota and account for increased susceptibility to disease onset or worsening of disease progression. In contrast, some environmental modifications through alternative therapies including fecal microbiota transplant (FMT), diet and dietary supplements with prebiotics, probiotics, and synbiotics have shown potential protective effects by reversing microbiota dysbiosis or by directly promoting beneficial microbes, together with minimal long-term adverse effects. In this review, we discuss the different approaches to modulating the global consortium of bacteria, fungi, viruses, and archaea in patients with CD through therapies that include antibiotics, probiotics, prebiotics, synbiotics, personalized diets, and FMT. We hope to provide evidence to encourage clinicians and researchers to incorporate these therapies into CD treatment options, along with making them aware of the limitations of these therapies, and indicate where more research is needed.
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Armstrong H, Bording-Jorgensen M, Valcheva R, Zhang Z, Jovel J, Petrova A, Carroll MW, Huynh HQ, Dieleman LA, Wine E. A47 MICROBIAL FUNCTIONS AS BIOMARKERS OF PRO-INFLAMMATORY RESPONSE TO SELECT DIETARY FIBERS IN IBD. J Can Assoc Gastroenterol 2022. [PMCID: PMC8859326 DOI: 10.1093/jcag/gwab049.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Dietary fibers are not digested in the bowel; they are fermented by microbes, typically promoting gut health. However, IBD patients experience sensitivity to consumption of fibers. Our previous findings offered the first mechanistic evidence demonstrating that unfermented dietary β-fructans (inulin and FOS) can induce pro-inflammatory cytokines in a subset of pediatric IBD colonic biopsies cultured ex vivo, and in the SYNERGY-1 (β-fructan) clinical study of adult remission UC patients. Incubating FOS with whole-microbiota intestinal washes from non-IBD or remission IBD patients improved fermentation and reduced pro-inflammatory responses, but not from patients with active disease. Fibre-induced immune responses correlated with microbe functions, luminal metabolites, and fibre avoidance.
Aims
Here we aimed to expand on our findings and define the role of microbial functions in mediating host response to β-fructans.
Methods
Colonic biopsies cultured ex vivo and cell lines in vitro were incubated with FOS (5g/L), or fermentation supernatants (24hr anaerobic fermentation). Immune responses (cytokine secretion [ELISA/MSD] and expression [qPCR]) were assessed. Taxonomic classification of microbial fermentation cultures was conducted with Kraken2 and metabolic profiling by HUMAnN2. HPLC and gas chromatography volatile fatty acid (CG-VFA) analysis were used to identify concentrations of remaining fibre and SCFAs following anaerobic fermentation.
Results
7 microbial enzymes were identified to be predictive of cytokine (IL-1β, IL23, IL-5, IL-8, MIP-1α) secretion in ex vivo colonic biopsies from pediatric Crohn disease (CD; n=38), ulcerative colitis (UC; n=20), and non-IBD (n=21) patients, in response to β-fructans; their use as biomarkers of response was determined in patient stool from the SYNERGY-1 clinical study cohort. Fermentation of FOS by whole-microbe intestinal washes from only non-IBD or remission IBD patients reduced cytokine secretion, and our findings demonstrate that this was due to a combination of reduction of β-fructan present and production of a precise combination of anti-inflammatory SCFAs.
Conclusions
Our findings suggest that intolerance and avoidance of fibers in select IBD patients is associated with the inability to ferment these fibers, mediated by altered microbial functions (enzymes), leading to worsened inflammation. Data indicate that gut microbial function, not composition, predicts patient pro-inflammatory response to β-fructans, supporting our hypothesis that overall community function impacts fibre fermentation and affects associated pro-inflammatory effects. Our work highlights select disease state scenarios in which administration of fermentable fibers should be avoided and tailored dietary interventions considered.
Funding Agencies
CIHRWeston Foundation, Mitacs
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Affiliation(s)
| | - M Bording-Jorgensen
- Pediatrics, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB, Canada
| | - R Valcheva
- University of Alberta, Edmonton, AB, Canada
| | - Z Zhang
- Jimei University, Xiamen, Fujian, China
| | - J Jovel
- University of Alberta, Edmonton, AB, Canada
| | - A Petrova
- University of Alberta, Edmonton, AB, Canada
| | - M W Carroll
- Pediatric Gastroenterology, Univeristy of Alberta, Edmonton, AB, Canada
| | - H Q Huynh
- Pediatrics, University of alberta, Edmonton, AB, Canada
| | - L A Dieleman
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - E Wine
- Pediatrics, University of alberta, Edmonton, AB, Canada
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Premraj N, Valcheva R, Dieleman LA. A230 ISOMALTODEXTRIN DOSE-DEPENDENTLY REDUCES COLITIS DEVELOPMENT IN HLA-B27 RAT COLITIS MODEL WITH ASSOCIATED CHANGES TO GUT MICROBIOME COMPOSITION AND SHORT CHAIN FATTY ACID PRODUCTION. J Can Assoc Gastroenterol 2021. [DOI: 10.1093/jcag/gwab002.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Inflammatory bowel disease (IBD) is characterized by altered intestinal microbiome (i.e. dysbiosis), described by reduced strict butyrate-producing anaerobes versus increased facultative anaerobes. Data from preclinical studies and clinical trials show prebiotic inulin-type fibers can prevent and reduce colitis. However, other dietary fibers (e.g. resistant starches, RS) are understudied and it is unknown if RS-induced microbial shifts are protective in experimental colitis.
Aims
Assess efficacy of isomaltodextrin (IMD), a novel RS, to reduce intestinal inflammation in HLA-B27 transgenic (TG) rat colitis model and identify protective mechanisms associated with gut microbial composition and function.
Methods
4 week old HLA-B27 TG rats were fed standard chow supplemented with: 7.5% IMD (low dose, LD), 15% IMD (high dose, HD), negative control (15% cellulose, NC), or positive control (15% fructooligosaccharides, PC) for 12 weeks. Body weight and food intake were measured. Cecal and colonic inflammation assessed by weight/length ratio, macroscopic scoring and mucosal IL-1β secretion. Changes in microbial energy metabolism evaluated by measuring short chain fatty acid (SCFA) production in stool and cecal contents. Endpoint fecal and cecal microbiota composition differences assessed by 16S rRNA gene sequencing (Illumina MiSeq platform).
Results
IMD showed dose-dependent effect on cecal inflammation, measured by macroscopic tissue scoring, weight/length ratio and IL-1β secretion. HD rats had significantly lower cecum IL-1β concentration compared to NC (q=0.01), while LD showed only a trend (q=0.09). HD had significantly higher cecal amounts of Bacteroidaceae and Allobaculum spp. and lower amounts of Peptostreptococcaceae, Eubacterium and Barnesiella spp. versus the LD and NC. HD was associated with significantly higher total SCFA compared to NC (q<0.01) and showed a trend of higher total SCFA than LD (q=0.06). Analysis of SCFAs revealed propionate, isobutyrate and valerate ratios were significantly lower in HD than LD and NC. HD showed a trend of higher ratio of butyrate + acetate compared to NC. This suggests increased carbohydrate fermentation by acetate-producing and -converting microbial groups. Correlation analysis confirmed IL-1β concentrations were positively associated with isobutyrate (r=0.52, q<0.01), valerate (r=0.54, q<0.01), and propionate (r=0.48, q<0.01), suggesting their use as chronic inflammation markers in HLA-B27 models.
Conclusions
IMD was dose-dependently effective in reducing chronic cecal inflammation in experimental colitis. Benefits were associated with specific shifts in gut microbiome composition and SCFA production. Results from this preclinical study warrant future microbiota-altering intervention trials using IMD in clinical IBD.
Funding Agencies
Hayashibara Co., Ltd.
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Affiliation(s)
- N Premraj
- Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB, Canada
| | - R Valcheva
- Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB, Canada
| | - L A Dieleman
- Medicine, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB, Canada
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Armstrong H, Valcheva R, Santer D, Zhang Z, Rieger A, Dijk SI, Dickner R, Jerasi J, Mander IK, Moreau F, Gorman H, Lafleur D, Jovel J, Petrova A, Chadee K, Carroll MW, Huynh HQ, Madsen K, Dieleman LA, Wine E. A31 COMPLEX ROLE OF DIETARY FIBERS IN IBD: MICROBES MEDIATE FIBER-INDUCED INFLAMMATION. J Can Assoc Gastroenterol 2021. [DOI: 10.1093/jcag/gwab002.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, typically promoting gut health. However, many IBD patients describe experiencing sensitivity to fibers. β-glucan, found on the surface of fungal cells during fungal infection, has been shown to bind to fiber receptors, such as Dectin-1, on host immune cells, resulting in a pro-inflammatory response. These fungal fibres share properties with dietary fibers.
Aims
As an altered gut microbial composition has been associated with IBD, we hypothesized that the loss of fiber-fermenting microbes populating the gut in IBD could lead to dietary fibers not being efficiently broken down into their beneficial biproducts (e.g. short chain fatty acids; SCFA), resulting in binding of intact fibers to pro-inflammatory host cell receptors.
Methods
Immune and epithelial cell lines and colonic biopsies cultured ex vivo were incubated with oligofructose or inulin (5g/L), or pre-fermented fibers (24hr anaerobic fermentation). Immune responses were measured by cytokine secretion (ELISA), and expression (qPCR). Barrier integrity was measured by transepithelial resistance (TEER). Food frequency questionnaire (FFQ) data of patient fiber consumption were correlated with gut microbes (shotgun sequencing) and immune responses to fiber in patient biopsies.
Results
Unfermented oligofructose induced IL-1β secretion in leukocytes (macrophage, T cell, neutrophil) and in colon biopsies from pediatric Crohn disease (CD; n=38) and ulcerative colitis (UC; n=20) patients cultured ex vivo, but not in non-IBD patients (n=21). IL-1β secretion was greater in patients with more severe disease. Pre-fermentation of oligofructose by whole-microbe intestinal washes from non-IBD patients or remission patients reduced secretion of IL-1β, while whole microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce cytokine secretion. Fiber effects on IL-1β secretion in biopsies positively correlated with effects on barrier integrity in T84 cells. Fiber-associated immune responses in patient biopsies cultured ex vivo (ELISA) correlated with fiber avoidance (FFQ) and gut microbiome (sequencing) in matching patient samples.
Conclusions
Our findings demonstrate that intolerance and avoidance of prebiotic fibers in select IBD patients is associated with the inability to ferment these fibers, leading to pro-inflammatory immune responses and intestinal barrier disruption. This highlights select disease state scenarios, in which administration of fermentable fibers should be avoided and tailored dietary interventions should be considered in IBD patients.
Funding Agencies
CIHRWeston Foundation
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Affiliation(s)
| | - R Valcheva
- University of Alberta, Edmonton, AB, Canada
| | - D Santer
- University of Alberta, Edmonton, AB, Canada
| | - Z Zhang
- University of Alberta, Edmonton, AB, Canada
| | - A Rieger
- University of Alberta, Edmonton, AB, Canada
| | - S I Dijk
- Physiology, University of Alberta, Edmonton, AB, Canada
| | - R Dickner
- University of Alberta, Edmonton, AB, Canada
| | - J Jerasi
- University of Alberta, Edmonton, AB, Canada
| | - I K Mander
- Pediatrics, University of Alberta, Beaumont, AB, Canada
| | - F Moreau
- University of Calgary, Calgary, AB, Canada
| | - H Gorman
- University of Calgary, Calgary, AB, Canada
| | - D Lafleur
- University of Alberta, Edmonton, AB, Canada
| | - J Jovel
- University of Alberta, Edmonton, AB, Canada
| | - A Petrova
- University of Alberta, Edmonton, AB, Canada
| | - K Chadee
- University of Calgary, Calgary, AB, Canada
| | - M W Carroll
- Pediatric Gastroenterology, Univeristy of Alberta, Edmonton, AB, Canada
| | - H Q Huynh
- Pediatrics, University of Alberta, Beaumont, AB, Canada
| | - K Madsen
- University of Alberta, Edmonton, AB, Canada
| | - L A Dieleman
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - E Wine
- Physiology, University of Alberta, Edmonton, AB, Canada
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Armstrong H, Dickner R, Rieger A, Mander IK, Jerasi J, Santer D, Valcheva R, Dijk SI, Petrova A, Dieleman LA, Carroll MW, Huynh HQ, Wine E. A15 MICROBES MEDIATE FIBER-INDUCED INFLAMMATION IN IBD. J Can Assoc Gastroenterol 2020. [DOI: 10.1093/jcag/gwz047.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The etiology of inflammatory bowel diseases (IBD) remains unknown, although gut microorganisms and diet have been implicated. Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, promoting gut health. However, many IBD patients describe experiencing sensitivity to fibres. Interestingly, fiber receptors on immune cells are able to interact with fibers typically found on the surface of fungal cells (which share properties with dietary fibers), for example, resulting in a paradoxical pro-inflammatory response.
Aims
As an altered microbial composition is a hallmark of IBD, we hypothesized that the loss of fiber fermenting-microbes populating the IBD gut could lead to dietary fibers not being efficiently broken down into their beneficial biproducts, resulting in binding of intact fibers to pro-inflammatory host cell receptors. This can ultimately drive pro-inflammatory responses and a microenvironment that promotes continued dysbiosis and increased pathogenicity of select microbes, as observed in IBD.
Methods
Fiber receptor expression gut was examined using immunohistochemistry and flow cytometry and demonstrated elevated receptor expression due to increased presence of immune cells in IBD patient biopsies. Cytokine secretion, in response to fiber (5mg/mL) or pre-fermented fibers, cultured with microbes of interest, was measured by ELISAs in cell lines in vitro and biopsy tissues cultured ex vivo.
Results
Whole-fibers induced pro-inflammatory cytokine production in macrophage, monocytes, and neutrophils. Specific microbes were capable of fermenting fiber, measured by gas chromatography. Pre-fermentation of fibers by these microbes reduced inflammatory cytokine production. The fiber oligofructose increased IL-1β in pediatric CD (n=44) and UC (n=29) biopsies cultured ex vivo but not in non-IBD (n=25). The increase was greater in patients with more severe disease. Pre-fermentation of oligofructose by bacteria reduced this secretion of IL-1β. Whole-microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce fiber-associated inflammation in macrophage cells compared to remission or non-IBD children. Statistical analysis of food frequency questionnaire (FFQ) data on fiber consumption demonstrated that fiber-associated inflammation in patient biopsies cultured ex vivo (ELISA and qPCR) correlated with fiber avoidance (FFQ).
Conclusions
Comparing in vitro findings to our patient FFQs, intestinal washes (microbe abundance), and detailed patient history will better define the relationship between microbes, dietary fibers, and gut inflammation in IBD. This will allow for tailored dietary intervention through dietary recommendations, prebiotic, and/or probiotic therapies.
Funding Agencies
CCCWeston Foundation, WCHRI
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Affiliation(s)
| | - R Dickner
- University of Alberta, Edmonton, AB, Canada
| | - A Rieger
- University of Alberta, Edmonton, AB, Canada
| | - I K Mander
- University of Alberta, Edmonton, AB, Canada
| | - J Jerasi
- University of Alberta, Edmonton, AB, Canada
| | - D Santer
- University of Alberta, Edmonton, AB, Canada
| | - R Valcheva
- University of Alberta, Edmonton, AB, Canada
| | - S I Dijk
- Physiology, University of Alberta, Edmonton, AB, Canada
| | - A Petrova
- University of Alberta, Edmonton, AB, Canada
| | - L A Dieleman
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - M W Carroll
- Pediatric Gastroenterology, Univeristy of Alberta, Edmonton, AB, Canada
| | - H Q Huynh
- Pediatrics, University of alberta, Edmonton, AB, Canada
| | - E Wine
- Pediatrics, University of Alberta, Edmonton, AB, Canada
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8
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Armstrong H, Bording-Jorgensen M, Jerasi J, Lafleur D, Valcheva R, Wine E. A45 MANAGING THE IBDO’S AND IBDON’TS OF DIETARY FIBER CONSUMPTION IN INFLAMMATORY BOWEL DISEASE. J Can Assoc Gastroenterol 2019. [DOI: 10.1093/jcag/gwz006.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - J Jerasi
- University of Alberta, Edmonton, AB, Canada
| | - D Lafleur
- University of Alberta, Edmonton, AB, Canada
| | - R Valcheva
- University of Alberta, Edmonton, AB, Canada
| | - E Wine
- Pediatrics, University of Alberta, Edmonton, AB, Canada
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Keshteli AH, Valcheva R, Nickurak C, Madsen K, Dieleman LA. A104 ASSOCIATION BETWEEN THE DIETARY INFLAMMATORY INDEX AND HIGH FECAL CALPROTECTIN IN ULCERATIVE COLITIS PATIENTS. J Can Assoc Gastroenterol 2019. [DOI: 10.1093/jcag/gwz006.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A H Keshteli
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - R Valcheva
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - C Nickurak
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - K Madsen
- Medicine, University of Alberta, Edmonton, AB, Canada
| | - L A Dieleman
- Medicine, University of Alberta, Edmonton, AB, Canada
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10
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Armstrong H, Alipour M, Valcheva R, Bording-Jorgensen M, Jovel J, Zaidi D, Shah P, Lou Y, Ebeling C, Mason AL, Lafleur D, Jerasi J, Wong GKS, Madsen K, Carroll MW, Huynh HQ, Dieleman LA, Wine E. Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases. Microbiome 2019; 7:1. [PMID: 30925932 PMCID: PMC6317230 DOI: 10.1186/s40168-018-0604-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/25/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically susceptible hosts. We hypothesized that host intestinal immunoglobulin (Ig) G can be used to identify bacteria involved in IBD pathogenesis. RESULTS IgG-bound and -unbound microorganisms were collected from 32 pediatric terminal ileum aspirate washes during colonoscopy [non-IBD (n = 10), Crohn disease (n = 15), and ulcerative colitis (n = 7)], and composition was assessed using the Illumina MiSeq platform. In vitro analysis of invasive capacity was evaluated by fluorescence in situ hybridization and gentamicin invasion assay; immune activation was measured by qPCR. Despite considerable inter-individual variations, IgG binding favored specific and unique mucosa-associated species in pediatric IBD patients. Burkholderia cepacia, Flavonifractor plautii, and Rumminococcus sp. demonstrated increased IgG binding, while Pseudomonas ST29 demonstrated reduced IgG binding, in IBD. In vitro validation confirmed that B. cepacia, F. plautii, and Rumminococcus display invasive potential while Pseudomonas protogens did not. CONCLUSION Using IgG as a marker of pathobionts in larger patient cohorts to identify microbes and elucidate their role in IBD pathogenesis will potentially underpin new strategies to facilitate development of novel, targeted diagnostic, and therapeutic approaches. Interestingly, this method can be used beyond the scope of this manuscript to evaluate altered gut pathobionts in a number of diseases associated with altered microbiota including arthritis, obesity, diabetes mellitus, alcoholic liver disease, cirrhosis, metabolic syndrome, and carcinomas.
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Affiliation(s)
- Heather Armstrong
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Misagh Alipour
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Rosica Valcheva
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Michael Bording-Jorgensen
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Physiology, University of Alberta, Edmonton, AB T6G 1C9 Canada
| | - Juan Jovel
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Deenaz Zaidi
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Prachi Shah
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Yuefei Lou
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Cory Ebeling
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Andrew L. Mason
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Dawson Lafleur
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Jeremy Jerasi
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Gane K.-S. Wong
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Karen Madsen
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Matthew W. Carroll
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Hien Q. Huynh
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
| | - Levinus A. Dieleman
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Eytan Wine
- CEGIIR, University of Alberta, Edmonton, AB T6G 2X8 Canada
- Department of Pediatrics, University of Alberta, Edmonton Clinic Health Academy, Room 4-577, 11405 87th Ave, Edmonton, AB T6G 1C9 Canada
- Department of Physiology, University of Alberta, Edmonton, AB T6G 1C9 Canada
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11
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Valcheva R, Koleva P, Martínez I, Walter J, Gänzle MG, Dieleman LA. Inulin-type fructans improve active ulcerative colitis associated with microbiota changes and increased short-chain fatty acids levels. Gut Microbes 2018; 10:334-357. [PMID: 30395776 PMCID: PMC6546336 DOI: 10.1080/19490976.2018.1526583] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The intestinal microbiota is involved in ulcerative colitis (UC) pathogenesis. Prebiotics are hypothesized to improve health through alterations to gut microbiota composition and/or activity. Our aim was therefore to determine if inulin-type fructans induce clinical benefits in UC, and identify if benefits are linked to compositional and/or functional shifts of the luminal (fecal) and mucosal (biopsy) bacterial communities. Patients (n = 25) with mild/moderately active UC received 7.5 g (n = 12) or 15 g (n = 13) daily oral oligofructose-enriched inulin (Orafti®Synergy1) for 9 weeks. Total Mayo score, endoscopic activity and fecal calprotectin were assessed. Fecal and mucosal bacterial communities were characterized by 16S rRNA tag sequencing, and short chain fatty acids (SCFA) production were measured in fecal samples. Fructans significantly reduced colitis in the high-dose group, with 77% of patients showing a clinical response versus 33% in the low-dose group (P = 0.04). Fructans increased colonic butyrate production in the 15 g/d dose, and fecal butyrate levels were negatively correlated with Mayo score (r = -0.50; P = 0.036). The high fructan dose led to an increased Bifidobacteriaceae and Lachnospiraceae abundance but these shifts were not correlated with improved disease scores. In summary, this pilot study revealed that 15 g/d dose inulin type fructans in UC produced functional but not compositional shifts of the gut microbiota, suggesting that prebiotic-induced alterations of gut microbiota metabolism are more important than compositional changes for the benefits in UC. The findings warrant future well-powered controlled studies for the use of β-fructans as adjunct therapy in patients with active UC.
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Affiliation(s)
- Rosica Valcheva
- Department of Medicine, Center of Excellence for Gastrointestinal Inflammation and Immunity Research, 7-142 Katz Group Centre, University of Alberta, Edmonton, Canada,CONTACT Rosica Valcheva Department of Medicine, CEGIIR Group, 7-142 Katz Group Centre, University of Alberta, AB T6G 2E1, Canada
| | - Petya Koleva
- Department of Dentistry, 7-096 Katz Group Centre, University of Alberta, Edmonton, Canada
| | - Inés Martínez
- Department of Agricultural, Food and Nutritional Science, 4-126A Li Ka Shing Centre for Health Research Innovation, University of Alberta, Edmonton, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, 4-126A Li Ka Shing Centre for Health Research Innovation, University of Alberta, Edmonton, Canada,Department of Biological Sciences, 7-142 Katz Group Centre, University of Alberta, Edmonton, Canada
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, Canada
| | - Levinus A. Dieleman
- Department of Medicine, Center of Excellence for Gastrointestinal Inflammation and Immunity Research, 7-142 Katz Group Centre, University of Alberta, Edmonton, Canada
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12
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Teshima CW, Goodman KJ, El-Kalla M, Turk S, El-Matary W, Valcheva R, Danchak R, Gordon M, Ho P, Mullins A, Wong D, Kao D, Meddings J, Huynh H, Dieleman LA. Increased Intestinal Permeability in Relatives of Patients With Crohn's Disease Is Not Associated With Small Bowel Ulcerations. Clin Gastroenterol Hepatol 2017; 15:1413-1418.e1. [PMID: 28286191 DOI: 10.1016/j.cgh.2017.02.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Many first-degree relatives of patients with Crohn's disease (CD) have increased intestinal permeability. Video capsule endoscopy (VCE) is the most sensitive imaging test to identify small bowel mucosal lesions that could indicate subclinical CD. We aimed to estimate the association of increased intestinal permeability with small bowel ulcerations detectable by VCE in healthy first-degree relatives of patients with CD. METHODS We conducted a cross-sectional study of 223 healthy, asymptomatic first-degree relatives of patients with CD (parents, siblings, and children; 9-45 years old) enrolled at the University of Alberta between 2009 and 2012. Patients were given the lactulose and mannitol test to measure small bowel permeability; we used high-performance liquid chromatography to measure concentrations of lactulose and mannitol in urine samples (increased permeability defined as a ratio of lactulose/mannitol 0.025 or greater). Patients with increased permeability (n = 39) and randomly selected subjects with normal permeability (n = 59) were then examined by VCE for signs of small bowel inflammation and subclinical CD. The prevalence of small bowel lesions was compared among groups. We performed logistic regression analyses to estimate odds ratios for the association of small bowel ulcerations with intestinal permeability. RESULTS Among 223 first-degree relatives of patients with CD, 30% were found to have increased intestinal permeability; VCE examination found 24% of subjects to have 3 or more small bowel ulcers. Three or more small bowel ulcers were detected in 28% of patients with increased intestinal permeability and 20% of patients with normal intestinal permeability (P = .37). The adjusted odds ratio for the association of 3 or more small bowel ulcers with increased intestinal permeability was 1.5 (95% confidence interval, 0.6-3.8; P = .46). CONCLUSIONS Thirty percent of healthy, asymptomatic first-degree relatives of patients with CD have increased intestinal permeability. However, a strong association of small bowel ulceration seen on VCE with increased intestinal permeability was not observed.
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Affiliation(s)
- Christopher W Teshima
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada; Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada
| | - Karen J Goodman
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed El-Kalla
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Samina Turk
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Wael El-Matary
- Section of Pediatric Gastroenterology, University of Manitoba, Winnipeg, Canada
| | - Rosica Valcheva
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Ronda Danchak
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Marilyn Gordon
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Peter Ho
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Amanda Mullins
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel Wong
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Dina Kao
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Meddings
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Hien Huynh
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Levinus A Dieleman
- Division of Gastroenterology and CEGIIR, University of Alberta, Edmonton, Alberta, Canada.
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13
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Keshteli AH, van den Brand FF, Madsen KL, Mandal R, Valcheva R, Kroeker KI, Han B, Bell RC, Cole J, Hoevers T, Wishart DS, Fedorak RN, Dieleman LA. Dietary and metabolomic determinants of relapse in ulcerative colitis patients: A pilot prospective cohort study. World J Gastroenterol 2017; 23:3890-3899. [PMID: 28638229 PMCID: PMC5467075 DOI: 10.3748/wjg.v23.i21.3890] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/05/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023] Open
Abstract
AIM To identify demographic, clinical, metabolomic, and lifestyle related predictors of relapse in adult ulcerative colitis (UC) patients.
METHODS In this prospective pilot study, UC patients in clinical remission were recruited and followed-up at 12 mo to assess a clinical relapse, or not. At baseline information on demographic and clinical parameters was collected. Serum and urine samples were collected for analysis of metabolomic assays using a combined direct infusion/liquid chromatography tandem mass spectrometry and nuclear magnetic resolution spectroscopy. Stool samples were also collected to measure fecal calprotectin (FCP). Dietary assessment was performed using a validated self-administered food frequency questionnaire.
RESULTS Twenty patients were included (mean age: 42.7 ± 14.8 years, females: 55%). Seven patients (35%) experienced a clinical relapse during the follow-up period. While 6 patients (66.7%) with normal body weight developed a clinical relapse, 1 UC patient (9.1%) who was overweight/obese relapsed during the follow-up (P = 0.02). At baseline, poultry intake was significantly higher in patients who were still in remission during follow-up (0.9 oz vs 0.2 oz, P = 0.002). Five patients (71.4%) with FCP > 150 μg/g and 2 patients (15.4%) with normal FCP (≤ 150 μg/g) at baseline relapsed during the follow-up (P = 0.02). Interestingly, baseline urinary and serum metabolomic profiling of UC patients with or without clinical relapse within 12 mo showed a significant difference. The most important metabolites that were responsible for this discrimination were trans-aconitate, cystine and acetamide in urine, and 3-hydroxybutyrate, acetoacetate and acetone in serum.
CONCLUSION A combination of baseline dietary intake, fecal calprotectin, and metabolomic factors are associated with risk of UC clinical relapse within 12 mo.
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14
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Alipour M, Zaidi D, Valcheva R, Jovel J, Martínez I, Sergi C, Walter J, Mason AL, Wong GKS, Dieleman LA, Carroll MW, Huynh HQ, Wine E. Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis. J Crohns Colitis 2016; 10:462-71. [PMID: 26660940 PMCID: PMC4946763 DOI: 10.1093/ecco-jcc/jjv223] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/03/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is associated with colonic mucosa barrier defects and bacterial dysbiosis, but these features may simply be the result of inflammation. Therefore, we sought to assess whether these features are inherently abrogated in the terminal ileum [TI] of UC patients, where inflammation is absent. METHODS TI biopsies from paediatric inflammatory bowel disease [IBD] subsets [Crohn's disease [CD; n = 13] and UC [n = 10]], and non-IBD disease controls [n = 12] were histologically graded, and alcian blue/periodic acid-Schiff stained biopsies were quantified. The mucosal barrier was assessed for mucin [MUC2], immunoglobulin [Ig]A, IgG, and total bacteria (fluorescence in-situ hybridisation [FISH probe EUB338]) by immunofluorescence. The regulation of mucin secretion was investigated by NLRP6 gene expression and immunofluorescence. The composition of the active mucosa-associated microbiota was explored by sequencing the 16S rRNA amplicon generated from total RNA. RESULTS Despite the absence of ileitis, UC patients displayed ileal barrier depletion illustrated by reductions in mucin-containing goblet cells and mucin production and altered epithelial NLRP6 expression. In both CD patients with ileitis and UC patients with normal histology, bacteria coated with IgA and IgG penetrated the TI mucin layer. Biopsy 16S rRNA sequencing revealed a reduction in α-diversity by three methods [Shannon, Simpson, and Equitability indices] between UC and non-IBD paediatric patients. CONCLUSIONS These findings suggest an underlying defect in the UC-afflicted intestinal tract even in the absence of inflammation, implicating barrier and microbial changes as primary abnormalities in UC that may play a causative role in disease development.
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Affiliation(s)
- Misagh Alipour
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Deenaz Zaidi
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Rosica Valcheva
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Juan Jovel
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Inés Martínez
- Department of Agriculture, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Jens Walter
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Agriculture, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Andrew L. Mason
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Gane Ka-Shu Wong
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada,Department of Biological Sciences, University of Alberta, Edmonton, Canada,Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Levinus A. Dieleman
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | | | - Hien Q. Huynh
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Eytan Wine
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada,Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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15
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Valcheva R, Dieleman LA. Prebiotics: Definition and protective mechanisms. Best Pract Res Clin Gastroenterol 2016; 30:27-37. [PMID: 27048894 DOI: 10.1016/j.bpg.2016.02.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 01/31/2023]
Abstract
The increase in chronic metabolic and immunologic disorders in the modern society is linked to major changes in the dietary patterns. These chronic conditions are associated with intestinal microbiota dysbiosis where important groups of carbohydrate fermenting, short-chain fatty acids-producing bacteria are reduced. Dietary prebiotics are defined as a selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health. Application of prebiotics may then restore the gut microbiota diversity and activity. Unlike the previously accepted prebiotics definition, where a limited number of bacterial species are involved in the prebiotic activity, new data from community-wide microbiome analysis demonstrated a broader affect of the prebiotics on the intestinal microbiota. These new findings require a revision of the current definition. In addition, prebiotics may exert immunomodulatory effects through microbiota-independent mechanisms that will require future investigations involving germ-free animal disease models.
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Affiliation(s)
- Rosica Valcheva
- Department of Medicine, Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, AB, Canada.
| | - Levinus A Dieleman
- Department of Medicine, Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, AB, Canada
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16
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Valcheva R, Hotte N, Gillevet P, Sikaroodi M, Thiessen A, Madsen KL. Soluble Dextrin Fibers Alter the Intestinal Microbiota and Reduce Proinflammatory Cytokine Secretion in Male IL-10-Deficient Mice. J Nutr 2015; 145:2060-6. [PMID: 26180249 DOI: 10.3945/jn.114.207738] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/22/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Prebiotic fibers stimulate the growth and activity of the gut microbiota. Interleukin 10-deficient (IL-10(-/-)) mice develop a colitis that is influenced by the gut microbial composition. OBJECTIVE The purpose of this study was to determine the effect of prebiotic fibers on the intestinal microbiota and immune function in IL-10(-/-) mice. METHODS At 4 wk of age, male IL-10(-/-) mice (n = 8/group) were randomly assigned to 5 diets: unpurified diet with cellulose (4%; control), corn-derived hydroxypropylated new resistant starch (NRS) (2% NRS + 2% cellulose), soluble fiber dextrin from tapioca (SFD-t) (4%), soluble fiber dextrin from corn (SFD-c) (4%), or soluble corn fiber (4%) for 12 wk. Growth, small intestinal permeability, histologic injury, intestinal cytokine secretion, and microbiota composition by 16S ribosomal RNA pyrosequencing of stool were measured. ANOVA and principal component analysis were applied to assess the fibers' effects. RESULTS There were no significant differences in mouse growth, intestinal weight, length, or gut permeability over the 12 wk feeding period. Mice fed dextrin-based diets secreted 47-88% less colonic IL-1β, tumor necrosis factor α, and IL-23 (SFD-t diet) and IL-12 heterodimer p70, IL-6, and chemokine ligand 1 (CXCL1) (SFD-c diet) (P < 0.05) than did the control group, whereas NRS-fed mice secreted 55-77% less IL-6 and CXCL1 (P < 0.05). Both SFD-t- and SFD-c-fed mice had a 70-75% lower abundance of Lactobacillaceae than control mice. The SFD-t diet group had a lower enterocyte injury score (P < 0.04) than did control mice, and this was associated with increased abundance of butyrate producers, including Incertae sedis XIV, Lachnospiraceae, and Ruminococcaceae (P < 0.001). CONCLUSIONS These results demonstrate that soluble prebiotic fibers selectively stimulate the growth of a distinctive gut microbiota in IL-10(-/-) mice. SFD-t induced the growth of butyrate-producing microbes and was effective in reducing proinflammatory cytokine secretion and enterocyte injury in this mouse model of colitis.
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Affiliation(s)
| | | | - Patrick Gillevet
- Department of Environmental Science, George Mason University, Fairfax, VA
| | - Masoumeh Sikaroodi
- Department of Environmental Science, George Mason University, Fairfax, VA
| | - Aducio Thiessen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada; and
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17
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Koleva P, Ketabi A, Valcheva R, Gänzle MG, Dieleman LA. Chemically defined diet alters the protective properties of fructo-oligosaccharides and isomalto-oligosaccharides in HLA-B27 transgenic rats. PLoS One 2014; 9:e111717. [PMID: 25369019 PMCID: PMC4219767 DOI: 10.1371/journal.pone.0111717] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/07/2014] [Indexed: 01/04/2023] Open
Abstract
Non-digestible oligosaccharides (NDO) were shown to reduce inflammation in experimental colitis, but it remains unclear whether microbiota changes mediate their colitis-modulating effects. This study assessed intestinal microbiota and intestinal inflammation after feeding chemically defined AIN-76A or rat chow diets, with or without supplementation with 8 g/kg body weight of fructo-oligosaccharides (FOS) or isomalto-oligosaccharides (IMO). The study used HLA-B27 transgenic rats, a validated model of inflammatory bowel disease (IBD), in a factorial design with 6 treatment groups. Intestinal inflammation and intestinal microbiota were analysed after 12 weeks of treatment. FOS and IMO reduced colitis in animals fed rat chow, but exhibited no anti-inflammatory effect when added to AIN-76A diets. Both NDO induced specific but divergent microbiota changes. Bifidobacteria and Enterobacteriaceae were stimulated by FOS, whereas copy numbers of Clostridium cluster IV were decreased. In addition, higher concentrations of total short-chain fatty acids (SCFA) were observed in cecal contents of rats on rat chow compared to the chemically defined diet. AIN-76A increased the relative proportions of propionate, iso-butyrate, valerate and iso-valerate irrespective of the oligosaccharide treatment. The SCFA composition, particularly the relative concentration of iso-butyrate, valerate and iso-valerate, was associated (P ≤ 0.004 and r ≥ 0.4) with increased colitis and IL-1 β concentration of the cecal mucosa. This study demonstrated that the protective effects of fibres on colitis development depend on the diet. Although diets modified specific cecal microbiota, our study indicates that these changes were not associated with colitis reduction. Intestinal inflammation was positively correlated to protein fermentation and negatively correlated with carbohydrate fermentation in the large intestine.
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Affiliation(s)
- Petya Koleva
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
| | - Ali Ketabi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Rosica Valcheva
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- School of Food and Pharmaceutical Engineering, Hubei University of Technology, Wuhan, China
| | - Levinus A. Dieleman
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
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Valcheva R, Yungareva T, Kirilov N, Dobreva G, Minkov I, Ivanova I. Proteolytic and Phytase Activity in Sourdough Lactic Acid Bacteria. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Sekwati-Monang B, Valcheva R, Gänzle MG. Microbial ecology of sorghum sourdoughs: Effect of substrate supply and phenolic compounds on composition of fermentation microbiota. Int J Food Microbiol 2012; 159:240-6. [DOI: 10.1016/j.ijfoodmicro.2012.09.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 09/07/2012] [Accepted: 09/19/2012] [Indexed: 02/06/2023]
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Valcheva R, Dieleman LA. Fructo-oligosaccharides as therapeutics for active Crohn's disease: adequate power and no effect. Inflamm Bowel Dis 2012; 18:391-2. [PMID: 21618354 DOI: 10.1002/ibd.21760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Rosica Valcheva
- Division of Gastroenterology Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
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Ferchichi M, Valcheva R, Prévost H, Onno B, Dousset X. A one-step reaction for the rapid identification of Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti using oligonucleotide primers designed from the 16S-23S rRNA intergenic sequences. J Appl Microbiol 2008; 104:1797-807. [PMID: 18217935 DOI: 10.1111/j.1365-2672.2007.03712.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AIMS Species-specific primers targeting the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR) were designed to rapidly discriminate between Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti species recently isolated from French sourdough. METHODS AND RESULTS The 16S-23S ISRs were amplified using primers 16S/p2 and 23S/p7, which anneal to positions 1388-1406 of the 16S rRNA gene and to positions 207-189 of the 23S rRNA gene respectively, Escherichia coli numbering (GenBank accession number V00331). Clone libraries of the resulting amplicons were constructed using a pCR2.1 TA cloning kit and sequenced. Species-specific primers were designed based on the sequences obtained and were used to amplify the 16S-23S ISR in the Lactobacillus species considered. For all of them, two PCR amplicons, designated as small ISR (S-ISR) and large ISR (L-ISR), were obtained. The L-ISR is composed of the corresponding S-ISR, interrupted by a sequence containing tRNA(Ile) and tRNA(Ala) genes. Based on these sequences, species-specific primers were designed and proved to identify accurately the species considered among 30 reference Lactobacillus species tested. CONCLUSIONS Designed species-specific primers enable a rapid and accurate identification of L. mindensis, L. paralimentarius, L. panis, L. pontis and L. frumenti species among other lactobacilli. SIGNIFICANCE AND IMPACT OF THE STUDY The proposed method provides a powerful and convenient means of rapidly identifying some sourdough lactobacilli, which could be of help in large starter culture surveys.
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Affiliation(s)
- M Ferchichi
- UMR INRA-1014 SECALIM, ENITIAA, Rue de la Géraudière, Nantes Cedex, France.
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Ferchichi M, Valcheva R, Prévost H, Onno B, Dousset X. Molecular identification of the microbiota of French sourdough using temporal temperature gradient gel electrophoresis. Food Microbiol 2007; 24:678-86. [PMID: 17613364 DOI: 10.1016/j.fm.2007.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 04/17/2007] [Accepted: 04/19/2007] [Indexed: 10/23/2022]
Abstract
The microbiota of four industrial French sourdoughs (BF, GO, VB and RF) was characterized by PCR temporal temperature gel electrophoresis (TTGE). The TTGE technique reveals differences in the 16S rDNA V6-V8 regions of these bacteria. DNA was extracted directly from sourdough samples. A specific TTGE fingerprint was determined for 30 bacterial species, including members of the genera Lactobacillus, Leuconostoc and Weissella, all known to be present in sourdough. These sourdoughs contain different species of lactic acid bacteria (LAB) depending on ecological conditions prevailing in the different sourdough fermentations. Only a few LAB species were found to be competitive and became dominant. Lactobacillus sanfranciscensis was observed as the most frequently found species. In sourdough GO, L. sanfranciscensis, Lactobacillus panis and two new species, Lactobacillus nantensis and Lactobacillus hammesii, were detected. Sourdough BF contain L. sanfranciscensis, Lactobacillus spicheri and Lactobacillus pontis. In sourdough VB, which differed in the process temperature, we identified exclusively L. sanfranciscensis and Leuconostoc mesenteroïdes subsp. mesenteroïdes. Lactobacillus frumenti, L. hammesii and Lacobacillus paralimentarius became the predominant species in sourdough RF. Compared with conventional bacteriological methods, the use of this new molecular approach to analyze the sourdough ecosystem should therefore allow a more complete and rapid assessment of its specific microbiota.
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MESH Headings
- Bread/microbiology
- Colony Count, Microbial
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Agar Gel/methods
- Fermentation
- Food Microbiology
- Lactobacillus/classification
- Lactobacillus/isolation & purification
- Leuconostoc/classification
- Leuconostoc/isolation & purification
- Phylogeny
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Species Specificity
- Temperature
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Affiliation(s)
- Mounir Ferchichi
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322, Nantes Cedex 3, France.
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23
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Valcheva R, Kabadjova P, Rachman C, Ivanova I, Onno B, Prévost H, Dousset X. A rapid PCR procedure for the specific identification of Lactobacillus sanfranciscensis, based on the 16S-23S intergenic spacer regions. J Appl Microbiol 2007; 102:290-302. [PMID: 17184346 DOI: 10.1111/j.1365-2672.2006.03039.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The organization of ribosomal RNA (rrn) operons in Lactobacillus sanfranciscensis was studied in order to establish an easy-to-perform method for identification of L. sanfranciscensis strains, based on the length and sequence polymorphism of the 16S-23S rDNA intergenic spacer region (ISR). METHODS AND RESULTS PCR amplification of the 16S-23S rDNA ISRs of L. sanfranciscensis gave three products distinguishing this micro-organism from the remaining Lactobacillus species. Sequence analysis revealed that two of the rrn operons were organized as in previously reported lactobacilli: large spacer (L-ISR), containing tRNA(Ile) and tRNA(Ala) genes; small spacer (S-ISR) without tRNA genes. The third described spacer (medium, M-ISR), original for L. sanfranciscensis, harboured a tRNA-like structure. An oligonucleotide sequence targeting the variable region between tDNA(Ile) and tDNA(Ala) of L. sanfranciscensis L-ISR was approved to be suitable in species-specific identification procedure. Analysis by pulse-field gel electrophoresis of the chromosomal digest with the enzyme I-CeuI showed the presence of seven rrn clusters. Lactobacillus sanfranciscensis genome size was estimated at c. 1.3 Mb. CONCLUSIONS Direct amplification of 16S-23S ISRs or PCR with specific primer derived from L-ISR showed to be useful for specific typing of L. sanfranciscensis. This was due to the specific rrn operon organization of L. sanfranciscensis strains. SIGNIFICANCE AND IMPACT OF THE STUDY In this paper, we have reported a rapid procedure for L. sanfranciscensis identification based on specific structures found in its rrn operon.
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Affiliation(s)
- R Valcheva
- Laboratoire de Microbiologie Alimentaire et Industrielle, QM2A, ENITIAA, Nantes Cedex 3, France.
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Valcheva R, Ferchichi MF, Korakli M, Ivanova I, Gänzle MG, Vogel RF, Prévost H, Onno B, Dousset X. Lactobacillus nantensis sp. nov., isolated from French wheat sourdough. Int J Syst Evol Microbiol 2006; 56:587-591. [PMID: 16514032 DOI: 10.1099/ijs.0.63619-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study of the bacterial flora isolated from traditional French wheat sourdough, using phenotypic characterization and phylogenetic as well as genetic methods, revealed a consistent group of isolates that could not be assigned to any recognized species. These results were confirmed by randomly amplified polymorphic DNA and amplified fragment length polymorphism fingerprinting analyses. Cells were Gram-positive, homofermentative rods. Comparative 16S rRNA gene sequence analysis of the representative strain LP33T indicated that these strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives Lactobacillus farciminis, Lactobacillus alimentarius, Lactobacillus paralimentarius and Lactobacillus mindensis. DNA–DNA reassociation experiments with the three phylogenetically closest Lactobacillus species confirmed that LP33T (=DSM 16982T=CIP 108546T=TMW 1.1265T) represents the type strain of a novel species, for which the name Lactobacillus nantensis sp. nov. is proposed.
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Affiliation(s)
- Rosica Valcheva
- Department of Microbiology, Faculty of Biology, University Sofia, 8 Dragan Tzankov Street, 1162 Sofia, Bulgaria
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Mounir F Ferchichi
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Maher Korakli
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Iskra Ivanova
- Department of Microbiology, Faculty of Biology, University Sofia, 8 Dragan Tzankov Street, 1162 Sofia, Bulgaria
| | - Michael G Gänzle
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Hervé Prévost
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Bernard Onno
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Xavier Dousset
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
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Tieking M, Kaditzky S, Valcheva R, Korakli M, Vogel RF, Gänzle MG. Extracellular homopolysaccharides and oligosaccharides from intestinal lactobacilli. J Appl Microbiol 2005; 99:692-702. [PMID: 16108811 DOI: 10.1111/j.1365-2672.2005.02638.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To characterize lactobacilli isolated from the intestines of ducks or pigs with respect to the production of extracellular homopolysaccharides (HoPS) and oligosaccharides. METHODS AND RESULTS Lactobacillus strains of duck or pig origin were screened for HoPS synthesis and >25% of the isolates produced fructans or glucans from sucrose. Glucan-forming strains were found within the species Lactobacillus reuteri and Lactobacillus animalis and fructan-forming strains were found within Lactobacillus mucosae, Lactobacillus crispatus and Lactobacillus acidophilus. The glucan-forming strains of L. reuteri but not L. animalis produced glucose-oligosaccharides in additon to the respective polymers, and two fructan-forming strains of L. acidophilus produced kestose. Genes coding for glycosyltransferases were detected by PCR and partially characterized by sequence analysis. CONCLUSIONS A large proportion of lactobacilli from intestinal habitats produce HoPS from sucrose and polysaccharide formation is generally associated with the formation of glucose- and fructose oligosaccharides. SIGNIFICANCE AND IMPACT OF THE STUDY The characterization of the metabolic potential of intestinal lactobacilli contributes to the understanding of the molecular basis of autochthony in intestinal habitats. Moreover, this is the first report of glucose-oligosaccharide production during growth of lactobacilli, and one novel fructosyltransferase and one novel glucansucrase were partially characterized on the genetic level.
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Affiliation(s)
- M Tieking
- TU München, Lehrstuhl für Technische Mikrobiologie, Freising, Germany
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Valcheva R, Korakli M, Onno B, Prévost H, Ivanova I, Ehrmann MA, Dousset X, Gänzle MG, Vogel RF. Lactobacillus hammesii sp. nov., isolated from French sourdough. Int J Syst Evol Microbiol 2005; 55:763-767. [PMID: 15774659 DOI: 10.1099/ijs.0.63311-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).
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Affiliation(s)
- Rosica Valcheva
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Maher Korakli
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Bernard Onno
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Hervé Prévost
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Iskra Ivanova
- Faculty of Biology, University of Sofia, Department of Microbiology, 8bul Dragan Tzankov, 1423 Sofia, Bulgaria
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Xavier Dousset
- Laboratoire de Microbiologie Alimentaire et Industrielle (LMAI), Unité de Recherche QM2A, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
| | - Michael G Gänzle
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
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Rachman C, Kabadjova P, Valcheva R, Prévost H, Dousset X. Identification of Carnobacterium species by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region and species-specific PCR. Appl Environ Microbiol 2004; 70:4468-77. [PMID: 15294774 PMCID: PMC492411 DOI: 10.1128/aem.70.8.4468-4477.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Accepted: 03/29/2004] [Indexed: 11/20/2022] Open
Abstract
The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in order to obtain restriction profiles for all of the species. Three PCR amplicons, which were designated small ISR (S-ISR), medium ISR (M-ISR), and large ISR (L-ISR), were obtained for all Carnobacterium species. The L-ISR sequence revealed the presence of two tRNA genes, tRNA(Ala) and tRNA(Ile), which were separated by a spacer region that varied from 24 to 38 bp long. This region was variable among the species, allowing the design of species-specific primers. These primers were tested and proved to be species specific. The identification method based on the 16S-23S rDNA ISR, using PCR-RFLP and specific primers, is very suitable for the rapid low-cost identification and discrimination of all of the Carnobacterium species from other phylogenetically related lactic acid bacteria.
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Affiliation(s)
- Cinta Rachman
- QM2A, LMAI, ENITIAA, rue de la Géraudière, BP 82225, 44322 Nantes Cedex 3, France
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Pantev A, Valcheva R, Danova S, Ivanova I, Minkov I, Haertlé T, Chobert JM. Effect of enterococcin A 2000 on biological and synthetic phospholipid membranes. Int J Food Microbiol 2003; 80:145-52. [PMID: 12381400 DOI: 10.1016/s0168-1605(02)00143-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Lactic acid bacterium isolated from Bulgarian cheese and identified as Enterococcus faecium produces a small hydrophobic peptide substance (enterococcin A 2000) with broad spectrum of antimicrobial activity. The wide range of enterococcin antibacterial activity of this compound against Gram-positive, as well as against some Gram-negative bacteria, suggests a single mechanism of action. The mode of action of enterococcin A 2000 was studied in intact liver mitochondria and synthetic phospholipid liposomes used as model systems. Enterococcin A 2000 stimulated the ATPase activity in intact mitochondria. The kinetic curve of ATP hydrolysis differed from that obtained in presence of dinitrophenol (DNP) and showed a character similar to the ATP hydrolysis in the presence of classic ionophores. Enterococcin A 2000, when bound to synthetic phospholipid liposomes, permeabilized liposomes liberating the marker carboxyfluorescein (CF).
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Affiliation(s)
- A Pantev
- Department of Microbiology, Faculty of Biology, University of Sofia, 8 bul. Dragan Tzankov, 1423, Sofia, Bulgaria.
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Pantev A, Kabadjova P, Valcheva R, Danova S, Dousset X, Haertlé T, Chobert JM, Ivanova I. Effects of nitrogen sources on bacteriocin production by Enterococcus faecium A 2000. Folia Microbiol (Praha) 2002; 47:659-62. [PMID: 12630315 DOI: 10.1007/bf02818667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The production of a novel broad-spectrum antimicrobial peptide enterococcin A 2000, active against Gram-positive and Gram-negative microorganisms including Listeria subsp. and Escherichia coli, by Enterococcus faecium strain A 2000 isolated from the surface of traditional Bulgarian yellow cheese "kash-kaval" is considerably influenced by complex nitrogen sources in the production medium. Medium components, especially peptone and yeast extract, and their concentration contributed to the increase in bacteriocin production during the stationary phase (16-46 h) of cultivation even in the absence of one of the components present in the basal cultivation MRS medium.
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Affiliation(s)
- A Pantev
- Department of Microbiology, Faculty of Biology, University of Sofia, 1423 Sofia, Bulgaria
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