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Harlow K, Summers KL, Oliver WT, Wells JE, Crouse M, Neville BW, Rempel LA, Rivera I, Ramsay TG, Davies CP. Weaning transition, but not the administration of probiotic candidate Kazachstania slooffiae, shaped the gastrointestinal bacterial and fungal communities in nursery piglets. Front Vet Sci 2024; 10:1303984. [PMID: 38274656 PMCID: PMC10808496 DOI: 10.3389/fvets.2023.1303984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
As in-feed antibiotics are phased out of swine production, producers are seeking alternatives to facilitate improvements in growth typically seen from this previously common feed additive. Kazachstania slooffiae is a prominent commensal fungus in the swine gut that peaks in relative abundance shortly after weaning and has beneficial interactions with other bacteriome members important for piglet health. In this study, piglets were supplemented with K. slooffiae to characterize responses in piglet health as well as fungal and bacterial components of the microbiome both spatially (along the entire gastrointestinal tract and feces) and temporally (before, during, and after weaning). Litters were assigned to one of four treatments: no K. slooffiae (CONT); one dose of K. slooffiae 7 days before weaning (day 14; PRE); one dose of K. slooffiae at weaning (day 21; POST); or one dose of K. slooffiae 7 days before weaning and one dose at weaning (PREPOST). The bacteriome and mycobiome were analyzed from fecal samples collected from all piglets at day 14, day 21, and day 49, and from organ samples along the gastrointestinal (GI) tract at day 21 and day 49. Blood samples were taken at day 14 and day 49 for cytokine analysis, and fecal samples were assayed for antimicrobial resistance. While some regional shifts were seen in response to K. slooffiae administration in the mycobiome of the GI tract, no remarkable changes in weight gain or health of the animals were observed, and changes were more likely due to sow and the environment. Ultimately, the combined microbiome changed most considerably following the transition from suckling to nursery diets. This work describes the mycobiome along the piglet GI tract through the weaning transition for the first time. Based on these findings, K. slooffiae administered at this concentration may not be an effective tool to hasten colonization of K. slooffiae in the piglet GI tract around the weaning transition nor support piglet growth, microbial gut health, or immunity. However, diet and environment greatly influence microbial community development.
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Affiliation(s)
- KaLynn Harlow
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - William T. Oliver
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - James E. Wells
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Matthew Crouse
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Bryan W. Neville
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Lea A. Rempel
- Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Israel Rivera
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Timothy G. Ramsay
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Cary Pirone Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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Antonsen J, Winther-Jensen M, Krogsbøll LT, Jess T, Jorgensen LN, Allin KH. Non-culture-based studies of the appendiceal microbiota: a systematic review. Future Microbiol 2023; 18:205-216. [PMID: 36916537 DOI: 10.2217/fmb-2022-0194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Aims: To review studies examining the appendiceal microbiota and microbial changes in acute appendicitis. Methods: After a systematic literature search, 11 studies examining the appendiceal microbiota (414 samples) using non-culture-based methods were included. Results: The appendiceal microbiota showed decreased α-diversity compared with fecal microbiota. Inflamed and uninflamed appendices showed differences in β-diversity, and there was an increased abundance of oral-associated bacteria in inflamed versus uninflamed appendices. Conclusion: The appendiceal microbiota exhibits lower α-diversity than the fecal microbiota, with an increased abundance of oral-associated bacteria. Compared with uninflamed appendices, the appendix microbiota in acute appendicitis also showed increased abundance of oral-associated bacteria, but no bacterial profile unique to either complicated or uncomplicated appendicitis was found.
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Affiliation(s)
- Jacob Antonsen
- Digestive Disease Centre, Bispebjerg & Frederiksberg Hospital, University of Copenhagen, Copenhagen, Denmark.,Department of Data, Biostatistics & Pharmacoepidemiology, Centre for Clinical Research & Prevention, Bispebjerg & Frederiksberg Hospital, Copenhagen, Denmark
| | - Matilde Winther-Jensen
- Department of Data, Biostatistics & Pharmacoepidemiology, Centre for Clinical Research & Prevention, Bispebjerg & Frederiksberg Hospital, Copenhagen, Denmark
| | - Lasse T Krogsbøll
- Digestive Disease Centre, Bispebjerg & Frederiksberg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Tine Jess
- Department of Clinical Medicine, Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Aalborg University, Copenhagen, Denmark.,Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Lars N Jorgensen
- Digestive Disease Centre, Bispebjerg & Frederiksberg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Kristine H Allin
- Department of Clinical Medicine, Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Aalborg University, Copenhagen, Denmark.,Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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Lee SHF, Ahmad SR, Lim YC, Zulkipli IN. The Use of Probiotic Therapy in Metabolic and Neurological Diseases. Front Nutr 2022; 9:887019. [PMID: 35592636 PMCID: PMC9110960 DOI: 10.3389/fnut.2022.887019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/29/2022] [Indexed: 12/20/2022] Open
Abstract
The human gut is home to trillions of microbes that interact with host cells to influence and contribute to body functions. The number of scientific studies focusing on the gut microbiome has exponentially increased in recent years. Studies investigating factors that may potentially affect the gut microbiome and may be used for therapeutic purposes in diseases where dysbioses in the gut microbiome have been shown are of particular interest. This review compiles current evidence available in the scientific literature on the use of probiotics to treat metabolic diseases and autism spectrum disorders (ASDs) to analyze the efficacy of probiotics in these diseases. To do this, we must first define the healthy gut microbiome before looking at the interplay between the gut microbiome and diseases, and how probiotics affect this interaction. In metabolic diseases, such as obesity and diabetes, probiotic supplementation positively impacts pathological parameters. Conversely, the gut–brain axis significantly impacts neurodevelopmental disorders such as ASDs. However, manipulating the gut microbiome and disease symptoms using probiotics has less pronounced effects on neurodevelopmental diseases. This may be due to a more complex interplay between genetics and the environment in these diseases. In conclusion, the use of microbe-based probiotic therapy may potentially have beneficial effects in ameliorating the pathology of various diseases. Validation of available data for the development of personalized treatment regimens for affected patients is still required.
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Pi Y, Hu J, Bai Y, Wang Z, Wu Y, Ye H, Zhang S, Tao S, Xiao Y, Han D, Ni D, Zou X, Wang J. Effects of dietary fibers with different physicochemical properties on fermentation kinetics and microbial composition by fecal inoculum from lactating sows in vitro. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:907-917. [PMID: 32737882 DOI: 10.1002/jsfa.10698] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Efficient utilization of dietary fibers (DFs) is important for optimizing feed resource utilization and animal health. The aim of the current study was to assess the effects of DFs with varying physicochemical properties (bulky, viscous, and fermentable) on fermentation kinetics and microbial composition during in vitro fermentation by fecal inoculum from lactating sow. According to the physicochemical properties, three different DFs, lignocellulose (LC), modified cassava starch (MCS) and konjac flour (KF) were selected as bulky fiber, fermentable fiber and viscous fiber respectively. Gas production, short-chain fatty acids (SCFAs) profiles and microbial composition were monitored during the fermentation. RESULTS Results showed that the gas production in 72 h (GP72h ) ranked as: KF > MCS > LC (P < 0.05). The halftime of asymptotic gas production ranked as: KF < MCS = LC (P < 0.001). At 36 h of fermentation, MCS group showed higher concentrations of formic acid and lactate than LC and KF groups, whereas KF group showed higher concentrations of propionate and butyrate than LC and MCS groups (P < 0.05). At 72 h of fermentation, KF group showed higher concentrations of formic acid, lactate and propionate than LC and MCS groups, whereas MCS group showed higher concentrations of acetate and butyrate than LC and KF groups (P < 0.05). At 36 h of fermentation, Anaerovibrio and Erysipelatoclostridium abundances were higher in KF group, whereas Proteiniclasticum abundance was higher in MCS group. At 72 h of fermentation, the abundance of Fibrobacter in LC group was higher than that in MCS and KF groups. In addition, we also observed that the abundances of certain specific bacteria (Anaerovibrio and Erysipelatoclostridium) were closely related to the SCFAs production (propionate and butyrate) at different fermentation times. CONCLUSION Collectively, the present study revealed that KF is a fast fermentation fiber which could produce propionate and butyrate rapidly, whereas LC is difficult to be fermented by bacteria. In addition, the fermentation of DFs with different physicochemical properties had divergent impacts on microbial composition and SCFA production. These findings deepen our understanding of the mechanisms of interaction between DFs and intestinal microbiota, and provide new ideas for the rational use of fiber resources in lactating sows. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Yu Pi
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Bai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhibo Wang
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Yujun Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Ye
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyi Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dongjiao Ni
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Xinhua Zou
- State Key Laboratory of Biological Feed, Ministry of Agriculture and Rural Affairs, Boen Biotechnology Co. Ltd, Ganzhou, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Christley S, Shogan B, Levine Z, Koo H, Guyton K, Owens S, Gilbert J, Zaborina O, Alverdy JC. Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis. PLoS One 2020; 15:e0232165. [PMID: 32343730 PMCID: PMC7188289 DOI: 10.1371/journal.pone.0232165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named “pre-op” isolates) and then 6 days later from the anastomotic site (herein named “post-op” isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.
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Affiliation(s)
- Scott Christley
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Benjamin Shogan
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Zoe Levine
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Hyun Koo
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Kristina Guyton
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Sarah Owens
- Argonne National Laboratory, Argonne, IL, United States of America
| | - Jack Gilbert
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
- Argonne National Laboratory, Argonne, IL, United States of America
| | - Olga Zaborina
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - John C. Alverdy
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
- * E-mail:
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6
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Bai F, Cai Z, Yang L. Recent progress in experimental and human disease-associated multi-species biofilms. Comput Struct Biotechnol J 2019; 17:1234-1244. [PMID: 31921390 PMCID: PMC6944735 DOI: 10.1016/j.csbj.2019.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 12/16/2022] Open
Abstract
Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown about the spatial organizations and interspecies interactions of individual species within the human microbiota. Bacterial cells tend to form surface-attached biofilms in many natural environments, which enable intercellular communications and interactions in a microbial ecosystem. In this review, we summarize the recent progresses on the experimental and human disease-associated multi-species biofilm studies. We hypothesize that engineering biofilm structures and interspecies interactions might provide a tool for manipulating the composition and function of human microbiota.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technology University, Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, China
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Pearce SC, Coia HG, Karl JP, Pantoja-Feliciano IG, Zachos NC, Racicot K. Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors. Front Physiol 2018; 9:1584. [PMID: 30483150 PMCID: PMC6240795 DOI: 10.3389/fphys.2018.01584] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 12/16/2022] Open
Abstract
The gut microbiome is extremely important for maintaining homeostasis with host intestinal epithelial, neuronal, and immune cells and this host-microbe interaction is critical during times of stress or disease. Environmental, nutritional, and cognitive stress are just a few factors known to influence the gut microbiota and are thought to induce microbial dysbiosis. Research on this bidirectional relationship as it pertains to health and disease is extensive and rapidly expanding in both in vivo and in vitro/ex vivo models. However, far less work has been devoted to studying effects of host-microbe interactions on acute stressors and performance, the underlying mechanisms, and the modulatory effects of different stressors on both the host and the microbiome. Additionally, the use of in vitro/ex vivo models to study the gut microbiome and human performance has not been researched extensively nor reviewed. Therefore, this review aims to examine current evidence concerning the current status of in vitro and ex vivo host models, the impact of acute stressors on gut physiology/microbiota as well as potential impacts on human performance and how we can parlay this information for DoD relevance as well as the broader scientific community. Models reviewed include widely utilized intestinal cell models from human and animal models that have been applied in the past for stress or microbiology research as well as ex vivo organ/tissue culture models and new innovative models including organ-on-a-chip and co-culture models.
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Affiliation(s)
- Sarah C Pearce
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Heidi G Coia
- National Research Council, The National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States.,711th Human Performance Wing, Airforce Research Laboratory, Airman Systems Directorate, Human-Centered ISR Division, Molecular Mechanisms Branch, Wright-Patterson Air Force Base, Dayton, OH, United States
| | - J P Karl
- Military Nutrition Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA, United States
| | - Ida G Pantoja-Feliciano
- Soldier Protection and Optimization Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kenneth Racicot
- Performance Nutrition Team, Combat Feeding Directorate, Natick Soldier Research, Development and Engineering Center, Natick, MA, United States
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Zhu H, Zeng D, Wang N, Niu LL, Zhou Y, Zeng Y, Ni XQ. Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR. AMB Express 2018; 8:68. [PMID: 29704067 PMCID: PMC5924506 DOI: 10.1186/s13568-018-0599-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/18/2018] [Indexed: 01/01/2023] Open
Abstract
The Sichuan takin (Budorcas taxicolor tibetana) is a rare and endangered ruminant distributed in the eastern Himalayas. However, little information is available regarding the intestinal microbiota of the takin. In this study, Illumina Miseq platform targeting the V4 region of the 16S rRNA was employed to characterize microbial community and diversity in the feces of wild (n = 6) and captive takins (n = 6). The takin exhibited an intestinal microbiota dominated by three phyla: Firmicutes (57.4%), Bacteroidetes (24.2%) and Proteobacteria (12.3%). At family/genus level, Ruminococcaceae, Bacteroidaceae, Acinetobacter, Clostridium, Lachnospiraceae, Rikenellaceae, Bacillus, Comamonas and Spirochaetaceae were dominant. Distinctive microbiotas between wild and captive takins were observed based on microbial community structure, captive takins having significantly higher community diversity. Quantitative real-time PCR were also utilized to monitor predominant bacteria in three Sichuan takin individuals housed in Chengdu Zoo over a half-year period, which showed that microbial communities of the three takins were relatively similar to each other and stable during our study period. Our results suggested that diet was a major driver for shaping microbial community composition.
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The Value of Fecal Microbiota Transplantation in the Treatment of Ulcerative Colitis Patients: A Systematic Review and Meta-Analysis. Gastroenterol Res Pract 2018; 2018:5480961. [PMID: 29849592 PMCID: PMC5903331 DOI: 10.1155/2018/5480961] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/16/2018] [Indexed: 12/14/2022] Open
Abstract
Background and Aims Fecal microbiota transplantation (FMT) has challenged the traditional management of ulcerative colitis (UC) in recent years, while it remained controversial. We aimed to provide a systematic protocol of FMT treatment on UC. Methods Studies reporting on FMT treatment in UC patients were performed. A fixed-effect model was used to assess the efficacy of FMT. Results Eighteen studies were enrolled (n = 446). A pooled proportion of patients who received FMT had a significant efficacy compared to the placebo group (odds ratio (OR): 2.73, P = 0.002) with a low risk of heterogeneity (P = 0.59, I2 = 0%). The Mayo score decreased to 5 points in a state of mild–moderate activity after FMT treatment, and the optimal range of the Mayo score baseline was 6–9 for FMT administration. Then, the baseline of the Shannon diversity index (SDI) had a negative correlation with the clinical response rate (R = −0.992, P = 0.08) or remission rate (R = −0.998, P = 0.036), and the optimal diversity of bacteria was at 7 days to one month. Moreover, the colonoscopy delivery and unrelated fecal donor had slight superiorities of FMT treatment. Conclusion FMT treatment had a higher efficacy and shorter time-point of early assessment of effectiveness on UC patients compared to traditional therapies. And the optimal FMT delivery and donor were colonoscopy delivery and unrelated donor in clinical practice.
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Shi Y, Dong Y, Huang W, Zhu D, Mao H, Su P. Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis. PLoS One 2016; 11:e0157259. [PMID: 27295210 PMCID: PMC4905678 DOI: 10.1371/journal.pone.0157259] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/26/2016] [Indexed: 02/06/2023] Open
Abstract
Background Fecal microbiota transplantation (FMT) has been recognized as a novel treatment for ulcerative colitis (UC). However, its efficacy and safety remain unclear. Objective We conducted this systematic review to assess the efficacy and safety of FMT in UC. Data Sources PubMed, EMBASE, Cochrane Central, Web of Science Core Collection, and three other Chinese databases were searched for reports of FMT in UC with clear outcomes. Data Extraction and Synthesis We estimated pooled rates [with 95% confidence interval (CI)] of clinical remission among 15 cohort studies and clinical response among 16 cohort studies. Results Twenty five studies (2 randomized controlled trials, 15 cohort studies, and 8 case studies) with 234 UC patients were included. Overall, 41.58% (84/202) patients achieved clinical remission (CR) and 65.28% (126/193) achieved clinical response. Among the cohort studies, the pooled estimate of patients who achieved CR and clinical response were 40.5% (95% CI 24.7%-58.7%), and 66.1% (95% CI 43.7%-83.0%). Most adverse events were slight and self-resolving. The analyses of gut microbiota in 7 studies showed that FMT could increase microbiota diversity and richness, similarity, and certain change of bacterial composition. Conclusion FMT provides a promising effect for UC with few adverse events. Successful FMT may be associated with an increase in microbiota diversity and richness, similarity, and certain change of bacterial composition.
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Affiliation(s)
- Yanqiang Shi
- The Second Clinical Medical School, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
| | - Yiwei Dong
- The Second Clinical Medical School, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
| | - Wenhui Huang
- The Second Clinical Medical School, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
| | - Decong Zhu
- The Second Clinical Medical School, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
| | - Hua Mao
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
| | - Peizhu Su
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, 510280, Guangzhou City, Guangdong Province, China
- * E-mail:
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11
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Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies. Sci Rep 2016; 6:26276. [PMID: 27188959 PMCID: PMC4870698 DOI: 10.1038/srep26276] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/25/2016] [Indexed: 01/12/2023] Open
Abstract
Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.
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12
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Hamasalim HJ. Synbiotic as Feed Additives Relating to Animal Health and Performance. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/aim.2016.64028] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Di Stasi LC, Costa CA, Witaicenis A. Products for the treatment of inflammatory bowel disease: a patent review (2013 - 2014). Expert Opin Ther Pat 2015; 25:629-42. [PMID: 25944127 DOI: 10.1517/13543776.2015.1041921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Inflammatory bowel disease (IBD) consists of Crohn's disease, ulcerative colitis and an unspecific IBD. The unclear etiology of IBD is a limiting factor that complicates the development of new pharmacological treatments and explains the high frequency of refractory patients to current drugs, including both conventional and biological therapies. In view of this, recent progress on the development of novel patented products to treat IBD was reviewed. AREAS COVERED Evaluation of the patent literature during the period 2013 - 2014 focused on chemical compounds, functional foods and biological therapy useful for the treatment of IBD. EXPERT OPINION Majority of the patents are not conclusive because they were based on data from unspecific methods not related to intestinal inflammation and, when related to IBD models, few biochemical and molecular evaluations that could be corroborating their use in human IBD were presented. On the other hand, methods and strategies using new formulations of conventional drugs, guanylyl cyclase C peptide agonists, compounds that influence anti-adhesion molecules, mAbs anti-type I interferons and anti-integrin, oligonucleotide antisense Smad7, growth factor neuregulin 4 and functional foods, particularly fermented wheat germ with Saccharomyces cerevisiae, are promising products for use in the very near future.
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Affiliation(s)
- Luiz C Di Stasi
- São Paulo State University (UNESP), Institute of Biosciences, Department of Pharmacology, Laboratory of Phytomedicines, Pharmacology and Biotechnology (PhytoPharmaTech) , 18.618-000 - Botucatu, São Paulo , Brazil +55 14 3880 0216 ;
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14
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Kim DH. Gut Microbiota-Mediated Drug-Antibiotic Interactions. Drug Metab Dispos 2015; 43:1581-9. [PMID: 25926432 DOI: 10.1124/dmd.115.063867] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022] Open
Abstract
Xenobiotic metabolism involves the biochemical modification of drugs and phytochemicals in living organisms, including humans and other animals. In the intestine, the gut microbiota catalyzes the conversion of hydrophilic drugs into absorbable, hydrophobic compounds through hydroxyzation and reduction. Drugs and phytochemicals are transformed into bioactive (sulfasalazine, lovastatin, and ginsenoside Rb1), bioinactive (chloramphenicol, ranitidine, and metronidazole), and toxic metabolites (nitrazepam), thus affecting the pharmacokinetics of the original compounds. Antibiotics suppress the activities of drug-metabolizing enzymes by inhibiting the proliferation of gut microbiota. Antibiotic treatment might influence xenobiotic metabolisms more extensively and potently than previously recognized and reduce gut microbiota-mediated transformation of orally administered drugs, thereby altering the systemic concentrations of intact drugs, their metabolites, or both. This review describes the effects of antibiotics on the metabolism of drugs and phytochemicals by the gut microbiota.
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Affiliation(s)
- Dong-Hyun Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Pharmacy, Kyung Hee University, Seoul, Republic of Korea
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15
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Yasir M, Angelakis E, Bibi F, Azhar EI, Bachar D, Lagier JC, Gaborit B, Hassan AM, Jiman-Fatani AA, Alshali KZ, Robert C, Dutour A, Raoult D. Comparison of the gut microbiota of people in France and Saudi Arabia. Nutr Diabetes 2015; 5:e153. [PMID: 25915742 PMCID: PMC4423199 DOI: 10.1038/nutd.2015.3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/27/2015] [Accepted: 03/15/2015] [Indexed: 12/18/2022] Open
Abstract
Background/Objectives: The gut microbiota contributes to energy acquisition from food, and changes in the gut microbiome are associated with obesity. The eating habits of Saudis are much different than those of Europeans, and our objective was to compare the fecal microbiota of obese and normal weight Saudis and French. Subjects/Methods: Illumina MiSeq deep sequencing was used to test the gut microbiota of 9 normal weight and 9 obese individuals from Saudi Arabia and 16 normal weight and 12 obese individuals from France. Results: Obese French possessed significantly more relative Proteobacteria (P=0.002) and Bacteroidetes (P=0.05) and had lower richness and biodiversity at all the operational taxonomic unit (OTU) cutoffs (P<0.05) than normal weight French. Obese Saudis possessed significantly more Firmicutes (P=0.001) without a difference in richness (P=0.2) and biodiversity (P=0.3) compared with normal weight Saudis. We found a common bacterial species core of 23 species existing in ⩾50% of obese and normal weight Saudis and 29 species in ⩾50% of obese and normal weight French. Actinomyces odontolyticus, Escherichia coli and Ruminococcus obeum were present in at least 50% of all individuals tested. French individuals had significantly higher richness and biodiversity compared with Saudis at all the OTU cutoffs (P<0.05). Conclusion: Microbiota differences between obese and normal weight French were not similar to those between obese and normal weight Saudis. The studies of different populations can result in contrasting data regarding the associations of the gut microbiota and obesity.
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Affiliation(s)
- M Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - F Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E I Azhar
- 1] Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia [2] Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - D Bachar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - B Gaborit
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
| | - A M Hassan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - A A Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - K Z Alshali
- Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - A Dutour
- Department of Endocrinology, Metabolic Diseases and Nutrition, CHU Nord, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Bringiotti R, Ierardi E, Lovero R, Losurdo G, Leo AD, Principi M. Intestinal microbiota: The explosive mixture at the origin of inflammatory bowel disease? World J Gastrointest Pathophysiol 2014; 5:550-559. [PMID: 25400998 PMCID: PMC4231519 DOI: 10.4291/wjgp.v5.i4.550] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/02/2014] [Accepted: 07/29/2014] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs), namely Crohn’s disease and ulcerative colitis, are lifelong chronic disorders arising from interactions among genetic, immunological and environmental factors. Although the origin of IBDs is closely linked to immune response alterations, which governs most medical decision-making, recent findings suggest that gut microbiota may be involved in IBD pathogenesis. Epidemiologic evidence and several studies have shown that a dysregulation of gut microbiota (i.e., dysbiosis) may trigger the onset of intestinal disorders such as IBDs. Animal and human investigations focusing on the microbiota-IBD relationship have suggested an altered balance of the intestinal microbial population in the active phase of IBD. Rigorous microbiota typing could, therefore, soon become part of a complete phenotypic analysis of IBD patients. Moreover, individual susceptibility and environmental triggers such as nutrition, medications, age or smoking could modify bacterial strains in the bowel habitat. Pharmacological manipulation of bowel microbiota is somewhat controversial. The employment of antibiotics, probiotics, prebiotics and synbiotics has been widely addressed in the literature worldwide, with the aim of obtaining positive results in a number of IBD patient settings, and determining the appropriate timing and modality of this intervention. Recently, novel treatments for IBDs, such as fecal microbiota transplantation, when accepted by patients, have shown promising results. Controlled studies are being designed. In the near future, new therapeutic strategies can be expected, with non-pathogenic or modified food organisms that can be genetically modified to exert anti-inflammatory properties.
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Abstract
Irritable bowel syndrome (IBS) is the most common gastrointestinal condition effecting adults in developed countries worldwide. Over the last decade, evidence has emerged suggesting that gut bacteria play a role in the pathophysiology of IBS. While difficult to identify using noninvasive means, one of the most common attributable bacterial concepts in IBS is the small intestinal bacterial overgrowth hypothesis (SIBO). In this article, we review the different mechanisms by which gut flora and, specifically, SIBO may contribute to IBS and the evidence supporting the use of various antibiotic therapies in treating IBS.
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18
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von Rosenvinge EC, O'May GA, Macfarlane S, Macfarlane GT, Shirtliff ME. Microbial biofilms and gastrointestinal diseases. Pathog Dis 2013; 67:25-38. [PMID: 23620117 DOI: 10.1111/2049-632x.12020] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/12/2012] [Accepted: 12/12/2012] [Indexed: 12/16/2022] Open
Abstract
The majority of bacteria live not planktonically, but as residents of sessile biofilm communities. Such populations have been defined as 'matrix-enclosed microbial accretions, which adhere to both biological and nonbiological surfaces'. Bacterial formation of biofilm is implicated in many chronic disease states. Growth in this mode promotes survival by increasing community recalcitrance to clearance by host immune effectors and therapeutic antimicrobials. The human gastrointestinal (GI) tract encompasses a plethora of nutritional and physicochemical environments, many of which are ideal for biofilm formation and survival. However, little is known of the nature, function, and clinical relevance of these communities. This review summarizes current knowledge of the composition and association with health and disease of biofilm communities in the GI tract.
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Affiliation(s)
- Erik C von Rosenvinge
- Department of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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19
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Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration. J Clin Microbiol 2012; 51:849-56. [PMID: 23269735 DOI: 10.1128/jcm.02574-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bacteria belonging to the normal colonic microbiota are associated with the etiology of ulcerative colitis (UC). Although several mucosal species have been implicated in the disease process, the organisms and mechanisms involved are unknown. The aim of this investigation was to characterize mucosal biofilm communities over time and to determine the relationship of these bacteria to patient age and disease severity and duration. Multiple rectal biopsy specimens were taken from 33 patients with active UC over a period of 1 year. Real-time PCR was used to quantify mucosal bacteria in UC patients compared to 18 noninflammatory bowel disease controls, and the relationship between indicators of disease severity and bacterial colonization was evaluated by linear regression analysis. Significant differences were detected in bacterial populations on the UC mucosa and in the control group, which varied over the study period. High clinical activity indices (CAI) and sigmoidoscopy scores (SS) were associated with enterobacteria, desulfovibrios, type E Clostridium perfringens, and Enterococcus faecalis, whereas the reverse was true for Clostridium butyricum, Ruminococcus albus, and Eubacterium rectale. Lactobacillus and bifidobacterium numbers were linked with low CAI. Only E. rectale and Clostridium clostridioforme had a high age dependence. These findings demonstrated that longitudinal variations in mucosal bacterial populations occur in UC and that bacterial community structure is related to disease severity.
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20
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Jonathan MC, van den Borne JJ, van Wiechen P, Souza da Silva C, Schols HA, Gruppen H. In vitro fermentation of 12 dietary fibres by faecal inoculum from pigs and humans. Food Chem 2012. [DOI: 10.1016/j.foodchem.2012.01.110] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Xie Y, Luo Z, Li Z, Deng M, Liu H, Zhu B, Ruan B, Li L. Structural shifts of fecal microbial communities in rats with acute rejection after liver transplantation. MICROBIAL ECOLOGY 2012; 64:546-554. [PMID: 22430504 DOI: 10.1007/s00248-012-0030-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/15/2012] [Indexed: 05/31/2023]
Abstract
Bacterial translocation and the development of sepsis after orthotopic liver transplantation (OLT) may be promoted by immunological damage to the intestinal mucosa or by quantitative and qualitative changes in intestinal microbiota. This study monitored structural shifts of gut microbiota in rats with OLT using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (RT-qPCR). RT-qPCR targets six major microorganisms (Domain Bacteria, Bacteroides, Bifidobacteria, Enterobacteriaceae, Lactobacillus and Clostridium leptum subgroup). Isograft, Allograft and Sham model were studied. Bacterial translocation to host organs and plasma endotoxin were determined. Alteration in gut microbiota was associated with the elevation of plasma endotoxin and a higher rate of bacterial translocation (BT) to liver in rats with acute rejection. Dynamic analysis of DGGE fingerprints showed that the gut microbiota structure of animals in the three groups was similar before the operation. But significant alterations in the composition of fecal microbiota in Allograft group were observed at 1 and 2 weeks after the OLT. The acute rejection was accompanied by the shifts of gut microbiota towards members of Bacteroides and Ruminococcus. Results from RT-qPCR indicated that Bacteroides significantly increased at 2 weeks after the OLT, whereas numbers of Bifidobacterium spp. decreased at 1 week and recovered at 2 weeks after the OLT. In summary, our data showed that rats with acute rejection after OLT exhibited significant structure shifts in the gut microbiota which dominant by overgrowth of Bacteroides and Ruminococcus, and these were associated with elevation of plasma endotoxin and higher rate of BT.
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Affiliation(s)
- Yirui Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 QingChun Road, Hangzhou, China, 310003
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Krajmalnik-Brown R, Ilhan ZE, Kang DW, DiBaise JK. Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract 2012; 27:201-14. [PMID: 22367888 DOI: 10.1177/0884533611436116] [Citation(s) in RCA: 477] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Malnutrition may manifest as either obesity or undernutrition. Accumulating evidence suggests that the gut microbiota plays an important role in the harvest, storage, and expenditure of energy obtained from the diet. The composition of the gut microbiota has been shown to differ between lean and obese humans and mice; however, the specific roles that individual gut microbes play in energy harvest remain uncertain. The gut microbiota may also influence the development of conditions characterized by chronic low-level inflammation, such as obesity, through systemic exposure to bacterial lipopolysaccharide derived from the gut microbiota. In this review, the role of the gut microbiota in energy harvest and fat storage is explored, as well as differences in the microbiota in obesity and undernutrition.
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Smith AR, Macfarlane GT, Reynolds N, O'May GA, Bahrami B, Macfarlane S. Effect of a synbiotic on microbial community structure in a continuous culture model of the gastric microbiota in enteral nutrition patients. FEMS Microbiol Ecol 2012; 80:135-45. [DOI: 10.1111/j.1574-6941.2011.01279.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/22/2023] Open
Affiliation(s)
- Aileen R. Smith
- Microbiology and Gut Biology Group; University of Dundee; Ninewells Hospital and Medical School; Dundee; UK
| | - George T. Macfarlane
- Microbiology and Gut Biology Group; University of Dundee; Ninewells Hospital and Medical School; Dundee; UK
| | - Nigel Reynolds
- Department of Gastroenterology; Ninewells Hospital and Medical School; Dundee; UK
| | - Graeme A. O'May
- Microbiology and Gut Biology Group; University of Dundee; Ninewells Hospital and Medical School; Dundee; UK
| | - Bahram Bahrami
- Microbiology and Gut Biology Group; University of Dundee; Ninewells Hospital and Medical School; Dundee; UK
| | - Sandra Macfarlane
- Microbiology and Gut Biology Group; University of Dundee; Ninewells Hospital and Medical School; Dundee; UK
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Pujol A, Crost EH, Simon G, Barbe V, Vallenet D, Gomez A, Fons M. Characterization and distribution of the gene cluster encoding RumC, an anti-Clostridium perfringens bacteriocin produced in the gut. FEMS Microbiol Ecol 2011; 78:405-15. [PMID: 22092178 DOI: 10.1111/j.1574-6941.2011.01176.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/08/2011] [Accepted: 07/11/2011] [Indexed: 11/26/2022] Open
Abstract
Ruminococcin C (RumC) is a trypsin-dependent bacteriocin produced by Ruminococcus gnavus E1, a gram-positive strict anaerobic strain isolated from human feces. It consists of at least three similar peptides active against Clostridium perfringens. In this article, a 15-kb region from R. gnavus E1 chromosome, containing the biosynthetic gene cluster of RumC was characterized. It harbored 17 open reading frames (called rum(c) genes) with predicted functions in bacteriocin biosynthesis and post-translational modification, signal transduction regulation, and immunity. An unusual feature of the locus is the presence of five genes encoding highly homologous, but nonidentical RumC precursors. The transcription levels of the rum(c) genes were quantified. The rumC genes were found to be highly expressed in vivo, when R. gnavus E1 colonized the digestive tract of mono-contaminated rats, whereas the amount of corresponding transcripts was below detection level when it grew in liquid culture medium. Moreover, the rumC-like genes were disseminated among 10 strains (R. gnavus or related species) previously isolated from human fecal samples and selected for their capability to produce a trypsin-dependant anti-C. perfringens compound. All harbored at least a rumC1-like copy, four exhibited rumC1-5 genes identical to those of strain E1.
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Affiliation(s)
- Ange Pujol
- ISM2/BiosCiences UMR CNRS 6263, Service 342, Faculté des Sciences et Techniques de St. Jérôme, Université Paul Cézanne Aix-Marseille III, Marseille, France
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25
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26
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Influence of food matrices on probiotic viability – A review focusing on the fruity bases. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.04.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Kunkel D, Basseri RJ, Makhani MD, Chong K, Chang C, Pimentel M. Methane on breath testing is associated with constipation: a systematic review and meta-analysis. Dig Dis Sci 2011; 56:1612-8. [PMID: 21286935 DOI: 10.1007/s10620-011-1590-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 01/21/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND A growing body of literature suggests an association between methane and constipation. Studies also link degree of methane production to severity of constipation and have shown constipation is improved following antibiotics. AIMS We aim to conduct a systematic review and meta-analysis to examine the cumulative evidence regarding the association between methane and constipation. METHODS A literature search was performed using MEDLINE and Embase to identify studies where the presence (or absence) of methane was assessed in constipated subjects. Search terms included "methane," "breath test," "constipation," "motility," "transit," "irritable bowel syndrome" and/or "IBS." Pooled odds ratios were generated using a random effects model. In a separate analysis, studies that measured intestinal transit in methane and non-methane subjects were systematically reviewed. RESULTS Nine studies met inclusion criteria for the meta-analysis. Among these, 1,277 subjects were examined by breath testing (N = 319 methane producers and N = 958 methane non-producers). Pooling all studies, a significant association was found between methane on breath test and constipation (OR = 3.51, CI = 2.00-6.16). Among adults only, methane was significantly associated with constipation (OR = 3.47, CI = 1.84-6.54). Similar results were seen when only examining subjects with IBS (OR = 3.60, CI = 1.61-8.06). The systematic review identified eight additional papers which all demonstrated an association between methane and delayed transit. CONCLUSIONS We demonstrate that methane present on breath testing is significantly associated with constipation in both IBS and functional constipation. These results suggest there may be merit in using breath testing in constipation. Moreover, methane may be used to identify candidates for antibiotic treatment of constipation.
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Affiliation(s)
- David Kunkel
- GI Motility Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Thalians Building, 2nd Floor East, Los Angeles, CA, 90048, USA
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Smith AR, Macfarlane S, Furrie E, Ahmed S, Bahrami B, Reynolds N, Macfarlane GT. Microbiological and immunological effects of enteral feeding on the upper gastrointestinal tract. J Med Microbiol 2011; 60:359-365. [DOI: 10.1099/jmm.0.026401-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Enteral feeding via a percutaneous endoscopic gastrostomy tube is required for nutritional support in patients with dysphagia. Enteral tube feeding bypasses the innate defence mechanisms in the upper gastrointestinal tract. This study examined the surface-associated microbial populations and immune response in the gastric and duodenal mucosae of eight enteral nutrition (EN) patients and ten controls. Real-time PCR and fluorescence in situ hybridization were employed to assess microbiota composition and mucosal pro-inflammatory cytokine expression. The results showed that EN patients had significantly higher levels of bacterial DNA in mucosal biopsies from the stomach and duodenum (P<0.05) than the controls, and that enterobacteria were the predominant colonizing species on mucosal surfaces in these individuals. Expression of the pro-inflammatory cytokines interleukin (IL)-1α, IL-6 and tumour necrosis factor-α was significantly higher in gastric and small intestinal mucosae from patients fed normal diets in comparison with those receiving EN (P<0.05). These results indicate that EN can lead to significant bacterial overgrowth on upper gastrointestinal tract mucosae and a significantly diminished pro-inflammatory cytokine response.
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Affiliation(s)
| | - Sandra Macfarlane
- Microbiology and Gut Biology Group, Ninewells Hospital and Medical School, Dundee, UK
| | - Elizabeth Furrie
- Microbiology and Gut Biology Group, Ninewells Hospital and Medical School, Dundee, UK
| | - Shakil Ahmed
- Microbiology and Gut Biology Group, Ninewells Hospital and Medical School, Dundee, UK
| | - Bahram Bahrami
- Microbiology and Gut Biology Group, Ninewells Hospital and Medical School, Dundee, UK
| | - Nigel Reynolds
- Gastroenterology Department, Ninewells Hospital and Medical School, Dundee, UK
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NELSON TA, HOLMES S, ALEKSEYENKO AV, SHENOY M, DESANTIS T, WU CH, ANDERSEN GL, WINSTON J, SONNENBURG J, PASRICHA PJ, SPORMANN A. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Neurogastroenterol Motil 2011; 23:169-77, e41-2. [PMID: 21129126 PMCID: PMC3353725 DOI: 10.1111/j.1365-2982.2010.01637.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. METHODS Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. KEY RESULTS Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. CONCLUSIONS & INFERENCES The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.
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Affiliation(s)
- T. A. NELSON
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA,Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA,Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA,Stanford University Bio-X Program, Stanford, CA, USA
| | - S. HOLMES
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - A. V. ALEKSEYENKO
- Department of Statistics, Stanford University, Stanford, CA, USA,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, NY, USA
| | - M. SHENOY
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - T. DESANTIS
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C. H. WU
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - G. L. ANDERSEN
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J. WINSTON
- Division of Gastroenterology, University of Texas Medical Branch, Galveston, TX, USA
| | - J. SONNENBURG
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - P. J. PASRICHA
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA,Stanford University Bio-X Program, Stanford, CA, USA,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - A. SPORMANN
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA,Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA,Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA,Stanford University Bio-X Program, Stanford, CA, USA
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Macfarlane S, Bahrami B, Macfarlane GT. Mucosal biofilm communities in the human intestinal tract. ADVANCES IN APPLIED MICROBIOLOGY 2011; 75:111-43. [PMID: 21807247 DOI: 10.1016/b978-0-12-387046-9.00005-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Complex and highly variable site-dependent bacterial ecosystems exist throughout the length of the human gastrointestinal tract. Until relatively recently, the majority of our information on intestinal microbiotas has come from studies on feces, or from aspirates taken from the upper gut. However, there is evidence showing that mucosal bacteria growing in biofilms on surfaces lining the gut differ from luminal populations, and that due to their proximity to the epithelial surface, these organisms may be important in modulating the host's immune system and contributing to some chronic inflammatory diseases. Over the past decade, increasing interest in mucosal bacteria, coupled with advances in molecular approaches for assessing microbial diversity, has begun to provide some insight into the complexity of these mucosa-associated communities. In gastrointestinal conditions such as inflammatory bowel diseases (ulcerative colitis, Crohn's disease), it has been shown that a dysbiosis exists in microbial community structure, and that there is a reduction in putatively protective mucosal organisms such as bifidobacteria. Therefore, manipulation of mucosal communities may be beneficial in restoring normal functionality in the gut, thereby improving the immune status and general health of the host. Biofilm structure and function has been studied intensively in the oral cavity, and as a consequence, mucosal communities in the mouth will not be covered in this chapter. This review addresses our current knowledge of mucosal populations in the gastrointestinal tract, changes that can occur in community structure in disease, and therapeutic modulation of biofilm composition by antibiotics, prebiotics, and probiotics.
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Affiliation(s)
- Sandra Macfarlane
- Microbiology and Gut Biology Group, University of Dundee, Dundee, United Kingdom.
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Pieper IA, Bertau M. Predictive tools for the evaluation of microbial effects on drugs during gastrointestinal passage. Expert Opin Drug Metab Toxicol 2010; 6:747-60. [DOI: 10.1517/17425251003769859] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gaggìa F, Mattarelli P, Biavati B. Probiotics and prebiotics in animal feeding for safe food production. Int J Food Microbiol 2010; 141 Suppl 1:S15-28. [PMID: 20382438 DOI: 10.1016/j.ijfoodmicro.2010.02.031] [Citation(s) in RCA: 446] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 02/04/2010] [Accepted: 02/28/2010] [Indexed: 01/16/2023]
Abstract
Recent outbreaks of food-borne diseases highlight the need for reducing bacterial pathogens in foods of animal origin. Animal enteric pathogens are a direct source for food contamination. The ban of antibiotics as growth promoters (AGPs) has been a challenge for animal nutrition increasing the need to find alternative methods to control and prevent pathogenic bacterial colonization. The modulation of the gut microbiota with new feed additives, such as probiotics and prebiotics, towards host-protecting functions to support animal health, is a topical issue in animal breeding and creates fascinating possibilities. Although the knowledge on the effects of such feed additives has increased, essential information concerning their impact on the host are, to date, incomplete. For the future, the most important target, within probiotic and prebiotic research, is a demonstrated health-promoting benefit supported by knowledge on the mechanistic actions. Genomic-based knowledge on the composition and functions of the gut microbiota, as well as its deviations, will advance the selection of new and specific probiotics. Potential combinations of suitable probiotics and prebiotics may prove to be the next step to reduce the risk of intestinal diseases and remove specific microbial disorders. In this review we discuss the current knowledge on the contribution of the gut microbiota to host well-being. Moreover, we review available information on probiotics and prebiotics and their application in animal feeding.
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Affiliation(s)
- Francesca Gaggìa
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, Bologna, Italy
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Oxalate-Degrading Bacteria of the Human Gut as Probiotics in the Management of Kidney Stone Disease. ADVANCES IN APPLIED MICROBIOLOGY 2010; 72:63-87. [DOI: 10.1016/s0065-2164(10)72003-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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McBain AJ, Madhwani T, Eatough J, Ledder R. An introduction to probiotics for dental health. ACTA ACUST UNITED AC 2009. [DOI: 10.1616/1476-2137.15748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Serino M, Luche E, Chabo C, Amar J, Burcelin R. Intestinal microflora and metabolic diseases. DIABETES & METABOLISM 2009; 35:262-72. [PMID: 19419895 DOI: 10.1016/j.diabet.2009.03.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 03/15/2009] [Indexed: 02/07/2023]
Abstract
Recent advances in molecular sequencing technology have allowed researchers to answer major questions regarding the relationship between a vast genomic diversity-such as found in the intestinal microflora-and host physiology. Over the past few years, it has been established that, in obesity, type 1 diabetes and Crohn's disease-to cite but a few-the intestinal microflora play a pathophysiological role and can induce, transfer or prevent the outcome of such conditions. A few of the molecular vectors responsible for this regulatory role have been determined. Some are related to control of the immune, vascular, endocrine and nervous systems located in the intestines. However, more important is the fact that the intestinal microflora-to-host relationship is bidirectional, with evidence of an impact of the host genome on the intestinal microbiome. This means that the ecology shared by the host and gut microflora should now be considered a new player that can be manipulated, using pharmacological and nutritional approaches, to control physiological functions and pathological outcomes. What now remains is to demonstrate the molecular connection between the intestinal microflora and metabolic diseases. We propose here that the proinflammatory lipopolysaccharides play a causal role in the onset of metabolic disorders.
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Affiliation(s)
- M Serino
- Institut national de la santé et de la recherche médicale, Toulouse, France.
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36
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The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm 2008; 363:1-25. [DOI: 10.1016/j.ijpharm.2008.07.009] [Citation(s) in RCA: 446] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 12/23/2022]
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Steed H, Macfarlane GT, Macfarlane S. Prebiotics, synbiotics and inflammatory bowel disease. Mol Nutr Food Res 2008; 52:898-905. [PMID: 18383235 DOI: 10.1002/mnfr.200700139] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The normal colonic microflora is intimately involved in the aetiology of inflammatory bowel diseases (IBD) such as ulcerative colitis (UC) and Crohn's disease (CD). These conditions are often refractile to conventional treatments involving the employment of anti-inflammatory and immunosuppressant drugs, and this has led to a search for alternative therapies based on the use of probiotics, prebiotics and synbiotics. The majority of investigations in this area have been done with probiotics, and while there is increasing interest in the abilities of prebiotics and synbiotics to control the symptoms of IBD, very few randomised controlled trials have been reported. Although the results have been variable, human and animal studies have demonstrated that in many circumstances, these functional foods can alter the composition of the colonic microbiota, reduce inflammatory processes in the gut mucosa, and have the potential to induce disease remission. More work is needed to understand the effects of prebiotics and synbiotics on microbial communities in the gut, and their interactions with the host's immune system.
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Affiliation(s)
- Helen Steed
- Gut Group, University of Dundee, Ninewells Hospital Medical School, Dundee, UK
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DiBaise JK, Zhang H, Crowell MD, Krajmalnik-Brown R, Decker GA, Rittmann BE. Gut microbiota and its possible relationship with obesity. Mayo Clin Proc 2008; 83:460-9. [PMID: 18380992 DOI: 10.4065/83.4.460] [Citation(s) in RCA: 347] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Obesity results from alterations in the body's regulation of energy intake, expenditure, and storage. Recent evidence, primarily from investigations in animal models, suggests that the gut microbiota affects nutrient acquisition and energy regulation. Its composition has also been shown to differ in lean vs obese animals and humans. In this article, we review the published evidence supporting the potential role of the gut microbiota in the development of obesity and explore the role that modifying the gut microbiota may play in its future treatment. Evidence suggests that the metabolic activities of the gut microbiota facilitate the extraction of calories from ingested dietary substances and help to store these calories in host adipose tissue for later use. Furthermore, the gut bacterial flora of obese mice and humans include fewer Bacteroidetes and correspondingly more Firmicutes than that of their lean counterparts, suggesting that differences in caloric extraction of ingested food substances may be due to the composition of the gut microbiota. Bacterial lipopolysaccharide derived from the intestinal microbiota may act as a triggering factor linking inflammation to high-fat diet-induced metabolic syndrome. Interactions among microorganisms in the gut appear to have an important role in host energy homeostasis, with hydrogen-oxidizing methanogens enhancing the metabolism of fermentative bacteria. Existing evidence warrants further investigation of the microbial ecology of the human gut and points to modification of the gut microbiota as one means to treat people who are over-weight or obese.
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Affiliation(s)
- John K DiBaise
- Division of Gastroenterology and Hepatology, Mayo Clinic, 13400 E Shea Blvd, Scottsdale, AZ 85259, USA.
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40
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Physiological aspects of energy metabolism and gastrointestinal effects of carbohydrates. Eur J Clin Nutr 2007; 61 Suppl 1:S40-74. [DOI: 10.1038/sj.ejcn.1602938] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ahmed S, Macfarlane GT, Fite A, McBain AJ, Gilbert P, Macfarlane S. Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol 2007; 73:7435-42. [PMID: 17890331 PMCID: PMC2168195 DOI: 10.1128/aem.01143-07] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Little is known about bacterial communities that colonize mucosal surfaces in the human gastrointestinal tract, but they are believed to play an important role in host physiology. The objectives of this study were to investigate the compositions of these populations in the distal small bowel and colon. Healthy mucosal tissue from either the terminal ileum (n = 6) or ascending (n = 8), transverse (n = 8), or descending colon (n = 4) of 26 patients (age, 68.5 +/- 1.2 years [mean +/- standard deviation]) undergoing emergency resection of the large bowel was used to study these communities. Mucosa-associated eubacteria were characterized by using PCR-denaturing gradient gel electrophoresis (DGGE), while real-time PCR was employed for quantitative analysis. Mucosal communities were also visualized in situ using confocal laser scanning microscopy. DGGE banding profiles from all the gut regions exhibited at least 45% homology, with five descending colon profiles clustering at ca. 75% concordance. Real-time PCR showed that mucosal bacterial population densities were highest in the terminal ileum and that there were no significant differences in overall bacterial numbers in different parts of the colon. Bifidobacterial numbers were significantly higher in the large bowel than in the terminal ileum (P = 0.006), whereas lactobacilli were more prominent in the distal large intestine (P = 0.019). Eubacterium rectale (P = 0.0004) and Faecalibacterium prausnitzii (P = 0.001) were dominant in the ascending and descending colon. Site-specific colonization in the gastrointestinal tract may be contributory in the etiology of some diseases of the large intestine.
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Affiliation(s)
- Shakil Ahmed
- Dundee University Gut Group, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
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Macfarlane GT, Macfarlane S. Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut. Curr Opin Biotechnol 2007; 18:156-62. [PMID: 17276052 DOI: 10.1016/j.copbio.2007.01.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 01/05/2007] [Accepted: 01/24/2007] [Indexed: 12/26/2022]
Abstract
There is increasing interest in the human colonic microbiota and in the way its metabolic activities impact on host health and well-being. For most practical purposes, however, the large bowel is inaccessible for routine investigation, and a variety of animal and in vitro model systems have been developed to study the microbiota. In vitro models range from simple closed systems using pure or defined mixed populations of bacteria, or faecal material, to more sophisticated complex multistage continuous cultures that are able to simulate many of the spatial, temporal and environmental attributes that characterize microbiological events in different regions of the large gut. Recent developments using these systems have enabled modelling of surface colonisation and biofilm development, a hitherto neglected area of study.
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Affiliation(s)
- George T Macfarlane
- Gut Group, University of Dundee, Ninewells Hospital Medical School, Dundee DD1 9SY, United Kingdom.
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Westall FC. Abnormal hormonal control of gut hydrolytic enzymes causes autoimmune attack on the CNS by production of immune-mimic and adjuvant molecules: A comprehensive explanation for the induction of multiple sclerosis. Med Hypotheses 2006; 68:364-9. [PMID: 16978797 DOI: 10.1016/j.mehy.2006.06.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 06/28/2006] [Accepted: 06/30/2006] [Indexed: 11/24/2022]
Abstract
Multiple sclerosis (MS) is generally thought to be caused by an autoimmune attack on central nervous system (CNS) myelin. A microorganism containing a mimic of an immunogenic region of a myelin protein initiates the autoimmune process. However, no specific "MS" microorganism has been found. Recently a large number of normal human gut bacteria were found to possess different encephalitogenic mimics. A hypothesis is presented that the autoimmune process is started by abnormal proteolytic digestion of these bacteria. Sufficient quantities of the mimics are produced to be recognized by the immune system. Since proteolytic processes in the gut are strictly controlled, it is proposed that the MS process is triggered by abnormal hormonal control of gut proteolytic enzymes. It has previously been suggested that the recognition of CNS myelin antigens by activated MS immune cells is facilitated by proteolytic processing of myelin proteins. The CNS proteases are also under rigid control and these control processes are the same as is in the gut. Therefore, MS clinical activity is the result of improper hydrolytic degradation in the brain-gut axis caused by an abnormal hormonal variation.
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Affiliation(s)
- Fred C Westall
- Institute for Disease Research, PO Box 890193, Temecula, CA 92589-0193, USA.
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Abstract
BACKGROUND Prebiotics are short-chain carbohydrates that alter the composition, or metabolism, of the gut microbiota in a beneficial manner. It is therefore expected that prebiotics will improve health in a way similar to probiotics, whilst at the same time being cheaper, and carrying less risk and being easier to incorporate into the diet than probiotics. AIM To review published evidence for prebiotic effects on gut function and human health. METHODS We searched the Science Citation Index with the terms prebiotic, microbiota, gut bacteria, large intestine, mucosa, bowel habit, constipation, diarrhoea, inflammatory bowel disease, Crohn's disease, ulcerative colitis, pouchitis, calcium and cancer, focussing principally on studies in humans and reports in the English language. Search of the Cochrane Library did not identify any clinical study or meta-analysis on this topic. RESULTS Three prebiotics, oligofructose, galacto-oligosaccharides and lactulose, clearly alter the balance of the large bowel microbiota by increasing bifidobacteria and Lactobacillus numbers. These carbohydrates are fermented and give rise to short-chain fatty acid and intestinal gas; however, effects on bowel habit are relatively small. Randomized-controlled trials of their effect in a clinical context are few, although animal studies show anti-inflammatory effects in inflammatory bowel disease, while calcium absorption is increased. CONCLUSIONS It is still early days for prebiotics, but they offer the potential to modify the gut microbial balance in such a way as to bring direct health benefits cheaply and safely.
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Affiliation(s)
- S Macfarlane
- Dundee University Gut Group, Division of Pathology and Neuroscience, Ninewells Hospital and Medical School, Dundee, UK.
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Franchini AG, Egli T. Global gene expression in Escherichia coli K-12 during short-term and long-term adaptation to glucose-limited continuous culture conditions. MICROBIOLOGY-SGM 2006; 152:2111-2127. [PMID: 16804185 DOI: 10.1099/mic.0.28939-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microarray technology was used to study the cellular events that take place at the transcription level during short-term (physiological) and long-term (genetic) adaptation of the faecal indicator bacterium Escherichia coli K-12 to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 h of glucose-limited continuous culture at a dilution rate of 0.3 h(-1) with those from batch culture with glucose excess. A large number of genes encoding periplasmic binding proteins were upregulated, indicating that the cells are prepared for high-affinity uptake of all types of carbon sources during glucose-limited growth in continuous culture. All the genes belonging to the maltose (mal/lamB) and galactose (mgl/gal) operons were upregulated. A similar transcription pattern was observed for long-term cultures except that the expression factors were lower than in the short-term adaptation. The patterns of upregulation were confirmed by real-time RT-PCR. A switch from a fully operational citric acid cycle to the PEP-glyoxylate cycle was clearly observed in cells grown in glucose-limited continuous culture when compared to batch-grown cells and this was confirmed by transcriptome analysis. This transcriptome analysis confirms and extends the observations from previous proteome and catabolome studies in the authors' laboratory.
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Affiliation(s)
- Alessandro G Franchini
- Swiss Federal Institute for Aquatic Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Thomas Egli
- Swiss Federal Institute for Aquatic Science and Technology, PO Box 611, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
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Child MW, Kennedy A, Walker AW, Bahrami B, Macfarlane S, Macfarlane GT. Studies on the effect of system retention time on bacterial populations colonizing a three-stage continuous culture model of the human large gut using FISH techniques. FEMS Microbiol Ecol 2006; 55:299-310. [PMID: 16420637 DOI: 10.1111/j.1574-6941.2005.00016.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fluorescence in situ hybridization was used to quantitate bacteria growing in a three-stage continuous culture system inoculated with human faeces, operated at two system retention times (60 and 20 h). Twenty-three different 16S rRNA gene oligonucleotide probes of varying specificities were used to detect bacteria. Organisms belonging to genera Bacteroides and Bifidobacterium, together with the Eubacterium rectale/Clostridium coccoides group, the Atopobium, Faecalibacterium prausnitzii and Eubacterium cylindroides groups, as well as the segmented filamentous bacteria, the Roseburia intestinalis group and lactic acid bacteria, were all present in high numbers in the continuous culture system. Other groups and species such as Ruminococci and Enterobacteria also persisted in the model, though not always at levels that allowed reliable quantitation. Some organisms such as Streptococci and Corynebacteria, present in the faecal inoculum, did not colonize the system. Other probes specific for Eubacterium lentum and for members of the genus Desulfovibrio did not detect these organisms at any time. Short chain fatty acid production was always highest in vessel I of the continuous culture system, however, a marked increase in acetate formation and a reduction in butyrate production occurred when system retention time was reduced to 20 h, which correlated with reductions in the numbers of butyrate-producing Roseburia.
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Affiliation(s)
- Matthew W Child
- Microbiology and Gut Biology Group, University of Dundee, Ninewells Hospital Medical School, Dundee, UK
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47
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Hofmann AF, Eckmann L. How bile acids confer gut mucosal protection against bacteria. Proc Natl Acad Sci U S A 2006; 103:4333-4. [PMID: 16537368 PMCID: PMC1450168 DOI: 10.1073/pnas.0600780103] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alan F Hofmann
- Department of Medicine, Division of Gastroenterology, University of California at San Diego, La Jolla, CA 92093-0813, USA.
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Macfarlane S, Woodmansey EJ, Macfarlane GT. Colonization of mucin by human intestinal bacteria and establishment of biofilm communities in a two-stage continuous culture system. Appl Environ Microbiol 2005; 71:7483-92. [PMID: 16269790 PMCID: PMC1287682 DOI: 10.1128/aem.71.11.7483-7492.2005] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 07/23/2005] [Indexed: 02/07/2023] Open
Abstract
The human large intestine is covered with a protective mucus coating, which is heavily colonized by complex bacterial populations that are distinct from those in the gut lumen. Little is known of the composition and metabolic activities of these biofilms, although they are likely to play an important role in mucus breakdown. The aims of this study were to determine how intestinal bacteria colonize mucus and to study physiologic and enzymatic factors involved in the destruction of this glycoprotein. Colonization of mucin gels by fecal bacteria was studied in vitro, using a two-stage continuous culture system, simulating conditions of nutrient availability and limitation characteristic of the proximal (vessel 1) and distal (vessel 2) colon. The establishment of bacterial communities in mucin gels was investigated by selective culture methods, scanning electron microscopy, and confocal laser scanning microscopy, in association with fluorescently labeled 16S rRNA oligonucleotide probes. Gel samples were also taken for analysis of mucin-degrading enzymes and measurements of residual mucin sugars. Mucin gels were rapidly colonized by heterogeneous bacterial populations, especially members of the Bacteroides fragilis group, enterobacteria, and clostridia. Intestinal bacterial populations growing on mucin surfaces were shown to be phylogenetically and metabolically distinct from their planktonic counterparts.
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Affiliation(s)
- Sandra Macfarlane
- Microbiology and Gut Biology Group, University of Dundee Medical School, Level 6, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, United Kingdom.
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