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Liu SH, Zhang Y, Guo ZX, Ayaz S, Wang YX, Huang ZH, Cao HH, Xu JP. Effects of baculovirus infection on intestinal microflora of BmNPV resistant and susceptible strain silkworm. JOURNAL OF ECONOMIC ENTOMOLOGY 2024:toae088. [PMID: 38706118 DOI: 10.1093/jee/toae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/05/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024]
Abstract
Bombyx mori L. (Lepidoptera: Bombycidae) nucleopolyhedrovirus (BmNPV) is a serious pathogen causing huge economic losses to sericulture. There is growing evidence that the gut microbiota of silkworms plays a critical role in shaping host responses and interactions with viral infection. However, little is known about the differences in the composition and diversity of intestinal microflora, especially with respect to silkworm strain differences and BmNPV infection-induced changes. Here, we aim to explore the differences between BmNPV-resistant strain A35 and susceptible strain P50 silkworm and the impact of BmNPV infection on intestinal microflora in different strains. The 16S rDNA sequencing analysis revealed that the fecal microbial populations were distinct between A35 and P50 and were significantly changed post BmNPV infection in both strains. Further analysis showed that the BmNPV-resistant strain silkworm possessed higher bacterial diversity than the susceptible strain, and BmNPV infection reduced the diversity of intestinal flora assessed by feces in both silkworm strains. In response to BmNPV infection, the abundance of Muribaculaceae increased in P50 and decreased in A35, while the abundance of Enterobacteriaceae decreased in P50 and increased in A35. These results indicated that BmNPV infection had various effects on the abundance of fecal microflora in different silkworm strains. Our findings not only broadened the understanding of host-pathogen interactions but also provided theoretical help for the breeding of resistant strains and healthy rearing of silkworms based on symbiotic bacteria.
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Affiliation(s)
- Shi-Huo Liu
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Ying Zhang
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Zhe-Xiao Guo
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Sadaf Ayaz
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Yan-Xiang Wang
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Zhi-Hao Huang
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Hui-Hua Cao
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
| | - Jia-Ping Xu
- Anhui Province Key Laboratory of Resource Insects Biology and Innovative Utilization, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, China
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Wu BY, Xu P, Cheng L, Wang QQ, Qiu HY, Yan XJ, Chen SL. The alteration of mucosal bile acid profile is associated with nerve growth factor expression in mast cells and bowel symptoms in diarrhea-predominant irritable bowel syndrome. Clin Exp Immunol 2024; 216:200-210. [PMID: 38290436 PMCID: PMC11036107 DOI: 10.1093/cei/uxae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/09/2023] [Accepted: 01/26/2024] [Indexed: 02/01/2024] Open
Abstract
Mucosal bile acid (BA) profile is still unestablished in diarrhea-predominant irritable bowel syndrome (IBS-D). The aim of this study was to explore colonic mucosal BAs and their associations with mucosal mast cell (MMC)-derived nerve growth factor (NGF) and bowel symptoms in IBS-D. Colonic mucosal biopsies from 36 IBS-D patients and 35 healthy controls (HCs) were obtained for targeted BA profiling. MMC count and the expression of NGF and tight junction proteins (TJPs) were examined. We found that colonic mucosal BA profile was altered in the IBS-D cohort. The proportion of primary BAs was significantly higher and that of secondary BAs was lower in IBS-D patients. According to the 90th percentile of total mucosal BA content of HCs, IBS-D patients were divided into BA-H (n = 7, 19.4%) and BA-L (n = 29, 80.6%) subgroups. BA-H patients showed significantly higher total mucosal BA content compared to BA-L subgroup and HCs. The mucosal content of 11 BA metabolites significantly increased in BA-H subgroup, e.g. cholic acid (CA) and taurocholic acid (TCA). Moreover, BA-H patients displayed significantly elevated MMC count and NGF expression, with decreased expression of TJPs (claudin-1, junctional adhesion molecule-A and zonula occludens-1). Correlation analyses revealed that mucosal TCA content positively correlated with MMC count, MMC-derived NGF levels, and abdominal pain while negatively correlated with TJP expression. In conclusion, IBS-D patients showed an altered BA profile in the colonic mucosa. Approximately 20% of them exhibit elevated mucosal BA content, which may be associated with MMC-derived NGF signaling and bowel symptoms.
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Affiliation(s)
- Bi-Yu Wu
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ping Xu
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Li Cheng
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qian-Qian Wang
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Hong-Yi Qiu
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiu-Juan Yan
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Sheng-Liang Chen
- Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Disease, Shanghai, China
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JohnBritto JS, Di Ciaula A, Noto A, Cassano V, Sciacqua A, Khalil M, Portincasa P, Bonfrate L. Gender-specific insights into the irritable bowel syndrome pathophysiology. Focus on gut dysbiosis and permeability. Eur J Intern Med 2024:S0953-6205(24)00105-5. [PMID: 38467533 DOI: 10.1016/j.ejim.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder involving the brain-gut interaction. IBS is characterized by persistent abdominal pain and changes in bowel habits. IBS exerts significant impacts on quality of life and imposes huge economic costs. Global epidemiological data reveal variations in IBS prevalence, both globally and between genders, necessitating comprehensive studies to uncover potential societal and cultural influences. While the exact pathophysiology of IBS remains incompletely understood, the mechanism involves a dysregulation of the brain-gut axis, leading to disturbed intestinal motility, local inflammation, altered intestinal permeability, visceral sensitivity, and gut microbiota composition. We reviewed several gender-related pathophysiological aspects of IBS pathophysiology, by focusing on gut dysbiosis and intestinal permeability. This perspective paves the way to personalized and multidimensional clinical management of individuals with IBS.
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Affiliation(s)
- Jerlin Stephy JohnBritto
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy
| | - Agostino Di Ciaula
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy
| | - Antonino Noto
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy
| | - Velia Cassano
- Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Angela Sciacqua
- Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Mohamad Khalil
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy
| | - Piero Portincasa
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy.
| | - Leonilde Bonfrate
- Clinica Medica "A. Murri", Department of Precision and Regenerative Medicine and Jonian Area (DiMePre-J), University of Bari Aldo Moro, Bari, Italy
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4
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Ho AHY, Lui RN. The current and future clinical applications of capsule endoscopy. J Gastroenterol Hepatol 2024; 39:28-33. [PMID: 38238541 DOI: 10.1111/jgh.16490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Affiliation(s)
- Agnes H Y Ho
- Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rashid N Lui
- Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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Zeng W, Chen Y, Zhang H, Peng L, Li Y, Liu B, Liang H, Du B, Li P. Probiotic-fermented Qushi decoction alleviates reserpine-induced spleen deficiency syndrome by regulating spleen function and gut microbiota dysbiosis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7702-7711. [PMID: 37439120 DOI: 10.1002/jsfa.12852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND Spleen deficiency syndrome (SDS) is associated with elevated inflammatory factors and dysregulation of gastrointestinal motility hormones and intestinal microbiota. Qushi decoction (QD), a traditional formula, has not been reported using modern scientific research methods for changes in its probiotic fermented QD (FQD) composition and its potential mechanisms to alleviate SDS. Therefore, the aim of this study was to investigate the splenic protection of FQD in SDS rats by modulating gastrointestinal motility hormones and intestinal microbiota. RESULTS The results showed that FQD increased total polysaccharides, total protein, total flavonoids and the other active ingredients compared to QD, effectively improved splenic inflammation and apoptosis in SDS rats, and modulated gastrointestinal motility hormones to alleviate diarrhea and other symptoms. In addition, the dysregulation of the gut microbiota was reversed by increasing the levels of Bifidobacterium and decreasing the levels of Escherichia-Shigella and Proteobacteria, which may be related to the regulation of bacterial metabolites to alleviate SDS. CONCLUSION These results suggest that FQD is an effective formula for improving SDS. Our findings show that FQD beneficial to the implications for the treatment of SDS. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Wenshen Zeng
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yang Chen
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Huan Zhang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Luwei Peng
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yaqi Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Bing Liu
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hongbo Liang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Bing Du
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Pan Li
- College of Food Science, South China Agricultural University, Guangzhou, China
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Gargari G, Mantegazza G, Taverniti V, Gardana C, Valenza A, Rossignoli F, Barbaro MR, Marasco G, Cremon C, Barbara G, Guglielmetti S. Fecal short-chain fatty acids in non-constipated irritable bowel syndrome: a potential clinically relevant stratification factor based on catabotyping analysis. Gut Microbes 2023; 15:2274128. [PMID: 37910479 PMCID: PMC10773536 DOI: 10.1080/19490976.2023.2274128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
The gut microbiota is believed to be a critical factor in the pathogenesis of IBS, and its metabolic byproducts, such as short-chain fatty acids (SCFAs), are known to influence gut function and host health. Despite this, the precise role of SCFAs in IBS remains a topic of debate. In this study, we examined the bacterial community structure by 16S rRNA gene profiling and SCFA levels by UPLC-MS/MS in fecal samples from healthy controls (HC; n = 100) and non-constipated patients (IBS-D and IBS-M; NC-IBS; n = 240) enrolled in 19 hospitals in Italy. Our findings suggest a significant difference between the fecal microbiomes of NC-IBS patients and HC subjects, with HC exhibiting higher intra-sample biodiversity. Furthermore, we were able to classify non-constipated patients into two distinct subgroups based on their fecal SCFA levels (fecal catabotype "high" and "low"), each characterized by unique taxonomic bacterial signatures. Our results suggest that the fecal catabotype with higher SCFA levels may represent a distinct clinical phenotype of IBS that could have implications for its diagnosis and treatment. This study provides a new perspective on the intricate relationship between the gut microbiome and bowel symptoms in IBS, underscoring the importance of personalized strategies for its management.
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Affiliation(s)
- Giorgio Gargari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Giacomo Mantegazza
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Valentina Taverniti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Claudio Gardana
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Alice Valenza
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Federico Rossignoli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Maria Raffaella Barbaro
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Marasco
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Cesare Cremon
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Barbara
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Simone Guglielmetti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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7
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Luo J, Wu YX, Ma LT, Zhang MY, Li FT, Cai YY, Zheng F, Yue H. Immunomodulatory effect of Liangyi paste on the gut microbiota of mice. J Pharm Biomed Anal 2023; 236:115706. [PMID: 37738734 DOI: 10.1016/j.jpba.2023.115706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/24/2023]
Abstract
Liangyi paste (LY) is a traditional Chinese medicine made from a mixture of Ginseng and Rehmanniae radix praeparata. The present study aimed to investigate the effects of LY on gut microbiota diversity in immunocompromised mice. The chemical composition of LY extract was analyzed using UPLC-Q-Orbitrap-MS/MS, and the differences in the structure and diversity of the intestinal microbiota of LY extract were examined using 16S rRNA. In this study, identified and analyzed 66 compounds from the LY. These compounds included 11 iridoids, 6 oligosaccharides, 21 protopanaxtriols, 23 protopanaxadiols, 2 OLE, 1 Ionone and 2 phenylethanoside, using advanced UPLC-Q-Orbitrap-MS/MS technology. Through the use of 16S rRNA analysis, the study found that LY significantly increased the relative abundance of the Firmicutes phylum in immunocompromised mice, while decreasing the abundance of the Proteobacteria and Actinobacteria phyla. At the genus level, LY significantly increased the relative abundance of beneficial bacteria such as Clostridium_sensu_stricto_l, Lactobacillus, and Limosilactobacillus in immunocompromised mice. Conversely, the paste extract decreased the relative abundance of harmful bacteria such as Enterococcus and Escherichia Shigella in immunocompromised mice. These findings highlight the potential of LY to serve as a natural dietary supplement for enhancing gut microbiota diversity and promoting gut health. The identification of numerous compounds within the paste extract demonstrates its complexity and potential as a source for further research and development. Additionally, the LY extract exerted a significant influence on both nucleotide and amino acid metabolism. To sum up, the findings suggest that the LY extract has the potential to modulate the structure and diversity of gut microbiota, as well as promote metabolic balance in immunocompromised mice.
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Affiliation(s)
- Jing Luo
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Yong-Xi Wu
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Li-Ting Ma
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Mei-Yu Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Fang-Tong Li
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Yong-Yu Cai
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China
| | - Fei Zheng
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China.
| | - Hao Yue
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, PR China.
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Napolitano M, Fasulo E, Ungaro F, Massimino L, Sinagra E, Danese S, Mandarino FV. Gut Dysbiosis in Irritable Bowel Syndrome: A Narrative Review on Correlation with Disease Subtypes and Novel Therapeutic Implications. Microorganisms 2023; 11:2369. [PMID: 37894027 PMCID: PMC10609453 DOI: 10.3390/microorganisms11102369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disorder characterized by chronic abdominal pain and altered bowel habits. It can be subclassified in different subtypes according to the main clinical manifestation: constipation, diarrhea, mixed, and unclassified. Over the past decade, the role of gut microbiota in IBS has garnered significant attention in the scientific community. Emerging research spotlights the intricate involvement of microbiota dysbiosis in IBS pathogenesis. Studies have demonstrated reduced microbial diversity and stability and specific microbial alterations for each disease subgroup. Microbiota-targeted treatments, such as antibiotics, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and even diet, offer exciting prospects for managing IBS. However, definitive conclusions are hindered by the heterogeneity of these studies. Further research should focus on elucidating the mechanisms, developing microbiome-based diagnostics, and enabling personalized therapies tailored to an individual's microbiome profile. This review takes a deep dive into the microscopic world inhabiting our guts, and its implications for IBS. Our aim is to elucidate the complex interplay between gut microbiota and each IBS subtype, exploring novel microbiota-targeted treatments and providing a comprehensive overview of the current state of knowledge.
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Affiliation(s)
- Maria Napolitano
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Ernesto Fasulo
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Federica Ungaro
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Luca Massimino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy;
| | - Silvio Danese
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Gastroenterology and Endoscopy, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesco Vito Mandarino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
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9
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Qu Y, Park SH, Dallas DC. The Role of Bovine Kappa-Casein Glycomacropeptide in Modulating the Microbiome and Inflammatory Responses of Irritable Bowel Syndrome. Nutrients 2023; 15:3991. [PMID: 37764775 PMCID: PMC10538225 DOI: 10.3390/nu15183991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a common gastrointestinal disorder marked by chronic abdominal pain, bloating, and irregular bowel habits. Effective treatments are still actively sought. Kappa-casein glycomacropeptide (GMP), a milk-derived peptide, holds promise because it can modulate the gut microbiome, immune responses, gut motility, and barrier functions, as well as binding toxins. These properties align with the recognized pathophysiological aspects of IBS, including gut microbiota imbalances, immune system dysregulation, and altered gut barrier functions. This review delves into GMP's role in regulating the gut microbiome, accentuating its influence on bacterial populations and its potential to promote beneficial bacteria while inhibiting pathogenic varieties. It further investigates the gut microbial shifts observed in IBS patients and contemplates GMP's potential for restoring microbial equilibrium and overall gut health. The anti-inflammatory attributes of GMP, especially its impact on vital inflammatory markers and capacity to temper the low-grade inflammation present in IBS are also discussed. In addition, this review delves into current research on GMP's effects on gut motility and barrier integrity and examines the changes in gut motility and barrier function observed in IBS sufferers. The overarching goal is to assess the potential clinical utility of GMP in IBS management.
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Affiliation(s)
- Yunyao Qu
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (Y.Q.); (S.H.P.)
- Nutrition Program, College of Health, Oregon State University, Corvallis, OR 97331, USA
| | - Si Hong Park
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (Y.Q.); (S.H.P.)
| | - David C. Dallas
- Department of Food Science & Technology, Oregon State University, Corvallis, OR 97331, USA; (Y.Q.); (S.H.P.)
- Nutrition Program, College of Health, Oregon State University, Corvallis, OR 97331, USA
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10
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Cheng Y, Huang X, Li L, Liu L, Zhang C, Fan X, Xie Y, Zou Y, Geng Z, Huang C. Effects of Solid Fermentation on Polygonatum cyrtonema Polysaccharides: Isolation, Characterization and Bioactivities. Molecules 2023; 28:5498. [PMID: 37513370 PMCID: PMC10384955 DOI: 10.3390/molecules28145498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Polygonati Rhizoma is a widely used traditional Chinese medicine (TCM) with complex pre-processing steps. Fermentation is a common method for processing TCM to reduce herb toxicity and enhance their properties and/or produce new effects. Here, in this study, using Bacillus subtilis and Saccharomyces cerevisiae, we aimed to evaluate the potential application of solid fermentation in isolating different functional polysaccharides from Polygonatum cyrtonema Hua. With hot water extraction, ethanol precipitation, DEAE anion exchange chromatography and gel filtration, multiple neutral and acidic polysaccharides were obtained, showing different yields, content, compositions and functional groups after fermentation. Combining in vitro experiments and in vivo aging and immunosuppressed mouse models, we further compared the antioxidant and immunomodulating bioactivities of these polysaccharides and found a prominent role of a natural polysaccharide (BNP) from fermented P. cyrtonema via Bacillus subtilis in regulating intestinal antioxidant defense and immune function, which may be a consequence of the ability of BNP to modulate the homeostasis of gut microbiota. Thus, this work provides evidence for the further development and utilization of P. cyrtonema with fermentation, and reveals the potential values of BNP in the treatment of intestinal disorders.
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Affiliation(s)
- Yi Cheng
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Xueyuan Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Lixia Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Lu Liu
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Chunsheng Zhang
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Xiang Fan
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Yu Xie
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Yuanfeng Zou
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhe Geng
- Department of Physical Education, Chengdu University of Information Technology, Chengdu 611130, China
| | - Chao Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
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11
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Dalis C, Mesfin FM, Manohar K, Liu J, Shelley WC, Brokaw JP, Markel TA. Volatile Organic Compound Assessment as a Screening Tool for Early Detection of Gastrointestinal Diseases. Microorganisms 2023; 11:1822. [PMID: 37512994 PMCID: PMC10385474 DOI: 10.3390/microorganisms11071822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Gastrointestinal (GI) diseases have a high prevalence throughout the United States. Screening and diagnostic modalities are often expensive and invasive, and therefore, people do not utilize them effectively. Lack of proper screening and diagnostic assessment may lead to delays in diagnosis, more advanced disease at the time of diagnosis, and higher morbidity and mortality rates. Research on the intestinal microbiome has demonstrated that dysbiosis, or unfavorable alteration of organismal composition, precedes the onset of clinical symptoms for various GI diseases. GI disease diagnostic research has led to a shift towards non-invasive methods for GI screening, including chemical-detection tests that measure changes in volatile organic compounds (VOCs), which are the byproducts of bacterial metabolism that result in the distinct smell of stool. Many of these tools are expensive, immobile benchtop instruments that require highly trained individuals to interpret the results. These attributes make them difficult to implement in clinical settings. Alternatively, electronic noses (E-noses) are relatively cheaper, handheld devices that utilize multi-sensor arrays and pattern recognition technology to analyze VOCs. The purpose of this review is to (1) highlight how dysbiosis impacts intestinal diseases and how VOC metabolites can be utilized to detect alterations in the microbiome, (2) summarize the available VOC analytical platforms that can be used to detect aberrancies in intestinal health, (3) define the current technological advancements and limitations of E-nose technology, and finally, (4) review the literature surrounding several intestinal diseases in which headspace VOCs can be used to detect or predict disease.
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Affiliation(s)
- Costa Dalis
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fikir M Mesfin
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Krishna Manohar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jianyun Liu
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - W Christopher Shelley
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - John P Brokaw
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Troy A Markel
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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12
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Dale HF, Lorentzen SCS, Mellin-Olsen T, Valeur J. Diet-microbiota interaction in irritable bowel syndrome: looking beyond the low-FODMAP approach. Scand J Gastroenterol 2023; 58:1366-1377. [PMID: 37384386 DOI: 10.1080/00365521.2023.2228955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Diet is one of the main modulators of the gut microbiota, and dietary patterns are decisive for gut-microbiota-related diseases, including irritable bowel syndrome (IBS). The low-FODMAP diet (LFD) is commonly used to treat IBS, but its long-term effects on microbiota, symptoms and quality of life (QoL) are unclear. Alternative dietary strategies promoting beneficial gut microbiota, combined with reduced symptoms and improved QoL, are therefore of interest. AIMS To review current evidence on the diet-microbiota-interaction as a modulator of IBS pathophysiology, and dietary management of IBS, with particular emphasis on strategies targeting the gut microbiota, beyond the LFD. METHODS Literature was identified through PubMed-searches with relevant keywords. RESULTS Dietary patterns with a low intake of processed foods and a high intake of plants, such as the Mediterranean diet, promote gut microbiota associated with beneficial health outcomes. In contrast, Western diets with a high intake of ultra-processed foods promote a microbiota associated with disease, including IBS. Increasing evidence points towards dietary strategies consistent with the Mediterranean diet being equal to the LFD in alleviating IBS-symptoms and having a less negative impact on QoL. Timing of food intake is suggested as a gut microbiota modulator, but little is known about its effects on IBS. CONCLUSIONS Dietary recommendations in IBS should aim to target the gut microbiota by focusing on improved dietary quality, considering the impact on both IBS-symptoms and QoL. Increased intake of whole foods combined with a regular meal pattern and limitation of ultra-processed foods can be beneficial strategies beyond the LFD.
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Affiliation(s)
- Hanna Fjeldheim Dale
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Clinical Support, Lovisenberg Diaconal Hospital, Oslo, Norway
| | | | - Tonje Mellin-Olsen
- Department of Clinical Support, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Jørgen Valeur
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Medicine, Lovisenberg Diaconal Hospital, Oslo, Norway
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13
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Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA. Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front Microbiol 2023; 14:1148097. [PMID: 37323911 PMCID: PMC10264612 DOI: 10.3389/fmicb.2023.1148097] [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: 01/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Aim The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids. Methods Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types. Results Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05). Conclusion Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.
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Affiliation(s)
- Christina Nowicki
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lucille Ray
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Philip Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Andrea Madrigrano
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Witt
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Lad
- Department of Oncology, Cook County Health and Hospital Systems, Chicago, IL, United States
| | - Melody Cobleigh
- Department of Internal Medicine, Division of Hematology, Oncology, and Cell Therapy, Rush University Medical Center, Chicago, IL, United States
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
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14
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Zhou D, Liu X, Lan L, Yu W, Qiu R, Wu J, Teng C, Huang L, Yu C, Zeng Y. Protective effects of Liupao tea against high-fat diet/cold exposure-induced irritable bowel syndrome in rats. Heliyon 2023; 9:e16613. [PMID: 37303551 PMCID: PMC10248097 DOI: 10.1016/j.heliyon.2023.e16613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
Liupao tea as a type of dark tea can relieve irritable bowel syndrome by regulating gut microbiota, but the mechanism has not been fully explained. An ultra-high performance liquid chromatography along with quadrupole time of flight tandem mass spectrometry was used to analyze the phytochemicals in Liupao tea. Then, we explored the effects of Liupao tea against IBS. From the results of chemical analysis, we identified catechins, polyphenols, amino acids, caffeine, polysaccharides and other components in Liupao tea. The open-field test, gastrointestinal function-related indexes, histochemical assays, measurements of cytokine and aquaporin 3 (AQP3), and determination of serum metabolites were utilized to monitor the physiological consequences of Liupao tea administration in rats with irritable bowel syndrome. The results showed that Liupao tea had a significant protective effect on irritable bowel syndrome. Liupao tea increased locomotive velocity while reducing interleukin-6, interleukin-1β, and tumor necrosis factor-α levels, as well as gastrointestinal injury. Moreover, Liupao tea increased the AQP3 levels of renal tissues but reduced the AQP3 levels of gastrointestinal tissues. Liupao tea reduced the Firmicutes/Bacteroides ratio and significantly reconstructed the microbial pattern. Liupao tea relieved irritable bowel syndrome by repairing gastrointestinal dysfunction, regulating the secretion of pro-inflammatory cytokines, modulating water metabolism, and restoring microbial homeostasis.
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Affiliation(s)
- Danshui Zhou
- School of Traditional Materia Medica, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xiaotong Liu
- School of Traditional Materia Medica, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Lunli Lan
- College of Pharmacy, Guilin Medical University, Guilin, Guangxi, China
| | - Wenxin Yu
- School of Traditional Materia Medica, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Ruijin Qiu
- Wuzhou Institute of Agricultural Sciences, Wuzhou, Guangxi, China
| | - Jianhua Wu
- Wuzhou Institute of Agricultural Sciences, Wuzhou, Guangxi, China
| | - Cuiqin Teng
- Wuzhou Institute of Agricultural Sciences, Wuzhou, Guangxi, China
| | - Liyun Huang
- Wuzhou Institute of Agricultural Sciences, Wuzhou, Guangxi, China
| | - Cuiping Yu
- Wuzhou Institute of Agricultural Sciences, Wuzhou, Guangxi, China
| | - Yu Zeng
- School of Traditional Materia Medica, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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15
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Goodoory VC, Ford AC. Antibiotics and Probiotics for Irritable Bowel Syndrome. Drugs 2023; 83:687-699. [PMID: 37184752 DOI: 10.1007/s40265-023-01871-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2023] [Indexed: 05/16/2023]
Abstract
Irritable bowel syndrome (IBS) is a disorder of a gut-brain interaction characterised by abdominal pain and a change in stool form or frequency. Current symptom-based definitions and the classification of IBS promote heterogeneity amongst patients, meaning that there may be several different pathophysiological abnormalities leading to similar symptoms. Although our understanding of IBS is incomplete, there are several indicators that the microbiome may be involved in a subset of patients. Techniques including a faecal sample analysis, colonic biopsies, duodenal aspirates or surrogate markers, such as breath testing, have been used to examine the gut microbiota in individuals with IBS. Because of a lack of a clear definition of what constitutes a healthy gut microbiota, and the fact that alterations in gut microbiota have only been shown to be associated with IBS, a causal relationship is yet to be established. We discuss several hypotheses as to how dysbiosis may be responsible for IBS symptoms, as well as potential treatment strategies. We review the current evidence for the use of antibiotics and probiotics to alter the microbiome in an attempt to improve IBS symptoms. Rifaximin, a non-absorbable antibiotic, is the most studied antibiotic and has now been licensed for use in IBS with diarrhoea in the USA, but the drug remains unavailable in many countries for this indication. Current evidence also suggests that certain probiotics, including Lactobacillus plantarum DSM 9843 and Bifidobacterium bifidum MIMBb75, may be efficacious in some patients with IBS. Finally, we describe the future challenges facing us in our attempt to modulate the microbiome to treat IBS.
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Affiliation(s)
- Vivek C Goodoory
- Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
- Leeds Gastroenterology Institute, St. James's University Hospital, Room 125, 4th Floor, Bexley Wing, Beckett Street, Leeds, LS9 7TF, UK
| | - Alexander C Ford
- Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, UK.
- Leeds Gastroenterology Institute, St. James's University Hospital, Room 125, 4th Floor, Bexley Wing, Beckett Street, Leeds, LS9 7TF, UK.
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16
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Zhao Y, Zou DW. Gut microbiota and irritable bowel syndrome. J Dig Dis 2023; 24:312-320. [PMID: 37458142 DOI: 10.1111/1751-2980.13204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/11/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that poses a significant health concern. Although its etiology remains unknown, there is growing evidence that gut dysbiosis is involved in the development and exacerbation of IBS. Previous studies have reported altered microbial diversity, abundance, and composition in IBS patients when compared to controls. However, whether dysbiosis or aberrant changes in the intestinal microbiota can be used as a hallmark of IBS remains inconclusive. We reviewed the literatures on changes in and roles of intestinal microbiota in relation to IBS and discussed various gut microbiota manipulation strategies. Gut microbiota may affect IBS development by regulating the mucosal immune system, brain-gut-microbiome interaction, and intestinal barrier function. The advent of high-throughput multi-omics provides important insights into the pathogenesis of IBS and promotes the development of individualized treatment for IBS. Despite advances in currently available microbiota-directed therapies, large-scale, well-organized, and long-term randomized controlled trials are highly warranted to assess their clinical effects. Overall, gut microbiota alterations play a critical role in the pathophysiology of IBS, and modulation of microbiota has a significant therapeutic potential that requires to be further verified.
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Affiliation(s)
- Ye Zhao
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Duo Wu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Kim GH, Lee K, Shim JO. Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets. Microbiol Spectr 2023; 11:e0212522. [PMID: 36652592 PMCID: PMC9927514 DOI: 10.1128/spectrum.02125-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Research on the gut microbiota in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. This study aimed to characterize how gut microbiota in IBS patients differs from that in healthy controls by performing a case-control study and cross- and mega-cohort analysis. Multiple publicly shared data sets were examined by using a unified analytical approach. We performed 16S rRNA gene (V3-4) sequencing and taxonomic profiling of the gut bacterial communities. Fecal samples from children with IBS (n = 19) and age-matched healthy controls (n = 24) were used. Next, we analyzed 10 separate data sets using a unified data-processing and analytical approach. In total, 567 IBS patients and 487 healthy controls were examined. In our data sets, no significant differences existed in stool α-diversity between IBS patients and healthy controls. After combining all the data sets using a unified data-processing method, we found significantly lower α-diversity in IBS patients than in healthy controls. In addition, the relative abundance of 21 bacterial species differed between the IBS patients and healthy participants. Although the causal relationship is uncertain, gut bacterial dysbiosis is associated with IBS. Further functional studies are needed to assess whether the change in gut microorganisms contributes to the development of IBS. IMPORTANCE Research on the gut bacteria in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. To overcome these issues, we analyzed microbiota of 567 IBS patients and 487 healthy people from 10 shared data sets using a unified method. We demonstrated that gut bacteria are less diverse in IBS patients than in healthy people. In addition, the abundance of 21 bacterial species is different between the two groups. Altered bacterial balance, called dysbiosis, has been reported in several disease states. Although the causal relationship is uncertain, gut bacterial dysbiosis also seems to be associated with IBS.
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Affiliation(s)
- Gun-Ha Kim
- Division of Pediatric Neurology, Department of Pediatrics, Korea Cancer Center Hospital, Korea Institute of Radiological & Medical Sciences, Seoul, South Korea
| | | | - Jung Ok Shim
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
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18
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Chen H, Ou R, Tang N, Su W, Yang R, Yu X, Zhang G, Jiao J, Zhou X. Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data. J Transl Med 2023; 21:117. [PMID: 36774467 PMCID: PMC9921069 DOI: 10.1186/s12967-023-03953-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/01/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive. METHOD A paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes. RESULTS A total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community. CONCLUSION This study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.
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Affiliation(s)
- Han Chen
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Rong Ou
- grid.411634.50000 0004 0632 4559Department of Gastroenterology and Hepatology, Jinhu County People’s Hospital, Huaian, China
| | - Nana Tang
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Wei Su
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Ruoyun Yang
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Guoxin Zhang
- grid.412676.00000 0004 1799 0784Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029 People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Jianhua Jiao
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China. .,The First Clinical Medical College, Nanjing Medical University, Nanjing, China.
| | - Xiaoying Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, 300# Guangzhou Road, Nanjing, 210029, People's Republic of China. .,The First Clinical Medical College, Nanjing Medical University, Nanjing, China.
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19
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Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates RA, Cheng A, March D, Hornig M, Komaroff AL, Levine S, Bateman L, Vernon SD, Klimas NG, Montoya JG, Peterson DL, Lipkin WI, Williams BL. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host Microbe 2023; 31:288-304.e8. [PMID: 36758522 PMCID: PMC10183837 DOI: 10.1016/j.chom.2023.01.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/10/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Amit Ranjan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Orchid Allicock
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Rachel A Yates
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Aaron Cheng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Dana March
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Anthony L Komaroff
- Division of General Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; Miami VA Medical Center, Miami, FL 33125, USA
| | - Jose G Montoya
- Palo Alto Medical Foundation, Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto, CA 94301, USA
| | - Daniel L Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV 89451, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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20
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Modulation of the microbiota across different intestinal segments by Rifaximin in PI-IBS mice. BMC Microbiol 2023; 23:22. [PMID: 36658488 PMCID: PMC9850553 DOI: 10.1186/s12866-023-02772-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 01/12/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Rifaximin has been increasingly applied in irritable bowel syndrome (IBS) treatment. Whether there were differences in the effects of rifaximin on microbiota from different intestinal segments, especially the small intestine where rifaximin predominantly acted, has not been confirmed. METHODS In this study, we used Trichinella spiralis infection to induce post infectious irritable bowel syndrome (PI-IBS) and measured visceral sensitivity of mice by means of abdominal withdrawal reflex (AWR) tests to colorectal distention (CRD). We compared the effects of rifaximin on the composition of ileal, colonic mucosal and fecal microbiota in PI-IBS mice. RESULTS Rifaximin significantly reduced AWR scores and increased pain threshold in PI-IBS mice, and this effect was associated with the change in the relative abundance of ileal mucosal microbiota. Rifaximin could obviously decrease ileum mucosal microbiota alpha diversity assessed by Shannon microbial diversity index. Meanwhile, the analysis of beta diversity and relative abundance of microbiota at phylum, family and genus levels showed that rifaximin could improve the microbiota structure of ileal mucosa. However, for colonic mucosal and fecal microbiota, this effect of rifaximin was not obvious. Rifaximin could reshape the correlation of genera between different intestinal segments. CONCLUSION Rifaximin improved visceral hypersensitivity in PI-IBS mice. Rifaximin mainly affected ileal mucosal microbiota, and its improvement effect on IBS might be closely related to the improvement of ileal microbiota structure.
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21
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Hou Y, Dong L, Lu X, Shi H, Xu B, Zhong W, Ma L, Wang S, Yang C, He X, Zhao Y, Wang S. Distinctions Between Fecal and Intestinal Mucosal Microbiota in Subgroups of Irritable Bowel Syndrome. Dig Dis Sci 2022; 67:5580-5592. [PMID: 35879512 DOI: 10.1007/s10620-022-07588-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/14/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND AND AIMS Recent studies have shown that changes in the intestinal microbiota contribute to the pathogenesis of irritable bowel syndrome (IBS). This study aimed to investigate the characteristics of the fecal and intestinal mucosal microbiota in IBS patients, and the correlation between microbiota and clinical manifestations. METHODS Fecal and intestinal mucosal samples were collected from 14 constipation-predominant IBS (IBS-C) patients, 20 diarrhea-predominant IBS (IBS-D) patients, and 20 healthy controls (HCs). 16S rRNA gene sequencing and fluorescence in situ hybridization were used for the analysis of samples. RESULTS Community richness and diversity of the fecal microbiota in IBS patients were significantly reduced compared with the HCs. The mucosal samples in IBS patients showed decreased Bifidobacterium and increased Bacteroides caccae compared with HCs; Eubacterium and Roseburia were decreased in IBS-C patients and increased in IBS-D patients. A comparison of the fecal and mucosal microbiota in IBS patients showed significantly increased Bifidobacterium in fecal samples and a decrease in mucosal samples in IBS-C patients; Bacteroides caccae and Roseburia were significantly reduced in fecal samples and increased in mucosal samples of IBS patients. A correlation between microbiota and clinical manifestations in IBS patients showed that Bacteroides caccae and Roseburia in fecal samples and Bifidobacterium and Eubacterium in mucosal samples were associated with abdominal pain and distention. CONCLUSIONS Distinct differences exist between the fecal and intestinal mucosal microbiota in IBS patients, with the changes in the latter appearing more consistent with the pathophysiology of IBS. Changes in intestinal microbiota were associated with the clinical manifestations in IBS.
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Affiliation(s)
- Yangfan Hou
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China.,Pulmonary and Critical Care Medicine, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Lei Dong
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Xiaolan Lu
- Department of Gastroenterology, Shanghai Pudong Hospital, Shanghai, 201399, China
| | - Haitao Shi
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Bing Xu
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Wenting Zhong
- International Medical Ward, Xi'an Jiaotong University Medical College First Affiliated Hospital, Xi'an, 710061, China
| | - Lin Ma
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Shuhui Wang
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Caifeng Yang
- Departments of Gastroenterology, Xi'an City First Hospital, Xi'an, 710002, China
| | - Xinyi He
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Yidi Zhao
- Emergency Department, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China
| | - Shenhao Wang
- Department of Gastroenterology, Xi'an Jiaotong University Second Affiliated Hospital, Xi'an, 710004, China.
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22
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Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
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Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
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23
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A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis. Pediatr Surg Int 2022; 38:1541-1553. [PMID: 35951092 DOI: 10.1007/s00383-022-05191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE Hirschsprung disease is a neurointestinal disease that occurs due to failure of enteric neural crest-derived cells to complete their rostrocaudal migration along the gut mesenchyme, resulting in aganglionosis along variable lengths of the distal bowel. Despite the effective surgery that removes the aganglionic segment, children with Hirschsprung disease remain at high risk for developing a potentially life-threatening enterocolitis (Hirschsprung-associated enterocolitis). Although the etiology of this enterocolitis remains poorly understood, several recent studies in both mouse models and in human subjects suggest potential involvement of gastrointestinal microbiota in the underlying pathogenesis of Hirschsprung-associated enterocolitis. METHODS We present the first study to exploit the Illumina MiSeq next-generation sequencing platform within a longitudinal framework focused on microbiomes of Hirschsprung-associated enterocolitis in five patients. We analyzed bacterial communities from fecal samples collected at different timepoints starting from active enterocolitis and progressing into remission. RESULTS We observed compositional differences between patients largely attributable to variability in age at the time of sample collection. Remission samples across patients exhibited compositional similarity, including enrichment of Blautia, while active enterocolitis samples showed substantial variability in composition. CONCLUSIONS Overall, our findings provide continued support for the role of GI microbiota in the pathogenesis of Hirschsprung-associated enterocolitis.
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24
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Relationship between mucosa-associated gut microbiota and human diseases. Biochem Soc Trans 2022; 50:1225-1236. [PMID: 36214382 PMCID: PMC9704521 DOI: 10.1042/bst20201201] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022]
Abstract
The mucus layer covering the gastrointestinal (GI) tract plays a critical role in maintaining gut homeostasis. In the colon, the inner mucus layer ensures commensal microbes are kept at a safe distance from the epithelium while mucin glycans in the outer mucus layer provide microbes with nutrients and binding sites. Microbes residing in the mucus form part of the so-called 'mucosa-associated microbiota' (MAM), a microbial community which, due to its close proximity to the epithelium, has a profound impact on immune and metabolic health by directly impacting gut barrier function and the immune system. Alterations in GI microbial communities have been linked to human diseases. Although most of this knowledge is based on analysis of the faecal microbiota, a growing number of studies show that the MAM signature differs from faecal or luminal microbiota and has the potential to be used to distinguish between diseased and healthy status in well-studied conditions such as IBD, IBS and CRC. However, our knowledge about spatial microbial alterations in pathogenesis remains severely hampered by issues surrounding access to microbial communities in the human gut. In this review, we provide state-of-the-art information on how to access MAM in humans, the composition of MAM, and how changes in MAM relate to changes in human health and disease. A better understanding of interactions occurring at the mucosal surface is essential to advance our understanding of diseases affecting the GI tract and beyond.
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25
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Beyoğlu D, Idle JR. The gut microbiota - a vehicle for the prevention and treatment of hepatocellular carcinoma. Biochem Pharmacol 2022; 204:115225. [PMID: 35998677 DOI: 10.1016/j.bcp.2022.115225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) arises principally against a background of cirrhosis and these two diseases are responsible globally for over 2 million deaths a year. There are few treatment options for liver cirrhosis and HCC, so it is vital to arrest these pathologies early in their development. To do so, we propose dietary and therapeutic solutions that involve the gut microbiota and its consequences. Integrated dietary, environmental and intrinsic signals result in a bidirectional connection between the liver and the gut with its microbiota, known as the gut-liver axis. Numerous lifestyle factors can result in dysbiosis with a change in the functional composition and metabolic activity of the microbiota. A panoply of metabolites can be produced by the microbiota, including ethanol, secondary bile acids, trimethylamine, indole, quinolone, phenazine and their derivatives and the quorum sensor acyl homoserine lactones that may contribute to HCC but have yet to be fully investigated. Gram-negative bacteria can activate the pattern recognition receptor toll-like receptor 4 (TLR4) in the liver leading to nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, which can contribute to HCC initiation and progression. The goal in preventing HCC should be to ensure a healthy gut microbiota using probiotic supplements containing beneficial bacteria and prebiotic plant fibers such as oligosaccharides that stimulate their growth. The clinical development of TLR4 antagonists is urgently needed to counteract the pathological effects of dysbiosis on the liver and other organs. Further nutrigenomic studies are required to understand better how the diet influences the gut microbiota and its adverse effects on the liver.
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Affiliation(s)
- Diren Beyoğlu
- Arthur G. Zupko Institute for Systems Pharmacology and Pharmacogenomics, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York 11201, USA
| | - Jeffrey R Idle
- Arthur G. Zupko Institute for Systems Pharmacology and Pharmacogenomics, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York 11201, USA.
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26
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Choo C, Mahurkar-Joshi S, Dong TS, Lenhart A, Lagishetty V, Jacobs JP, Labus JS, Jaffe N, Mayer EA, Chang L. Colonic mucosal microbiota is associated with bowel habit subtype and abdominal pain in patients with irritable bowel syndrome. Am J Physiol Gastrointest Liver Physiol 2022; 323:G134-G143. [PMID: 35726867 PMCID: PMC9359639 DOI: 10.1152/ajpgi.00352.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mucosal microbiota differ significantly from fecal microbiota and may play a different role in the pathophysiology of irritable bowel syndrome (IBS). The aims of this study were to determine if the composition of mucosal microbiota differed between IBS, or IBS bowel habit (BH) subtypes, and healthy controls (HCs). Sigmoid colon mucosal biopsies were obtained from 97 Rome-positive patients with IBS (28% IBS-constipation, 38% IBS-diarrhea, 24% IBS-mixed, and 10% IBS-unsubtyped) and 54 HCs, from which DNA was extracted. 16S rRNA gene sequencing and microbial composition analysis were performed. Group differences in α and β diversity and taxonomic level differences were determined using linear regression while controlling for confounding variables. IBS BH subtype was associated with microbial α diversity (P = 0.0003) with significant differences seen in the mucosal microbiota of IBS-constipation versus IBS-diarrhea (P = 0.046). There were no significant differences in α or β diversity in the mucosal microbiota of IBS versus HCs (P = 0.29 and 0.93, respectively), but metagenomic profiling suggested functional differences. The relative abundance of Prevotella_9 copri within IBS was significantly correlated with increased abdominal pain (r = 0.36, P = 0.0003), which has not been previously reported in IBS. Significant differences in the mucosal microbiota were present within IBS BH subtypes but not between IBS and HCs, supporting the possibility of IBS BH subtype-specific pathogenesis. Increased Prevotella copri may contribute to symptoms in patients with IBS.NEW & NOTEWORTHY Gut mucosal microbiota differs significantly from fecal microbiota in irritable bowel syndrome (IBS) and may play a different role in its pathophysiology. Investigation of colonic mucosal microbiota in the largest cohort of patients with IBS and healthy controls accounting for confounding variables, including diet demonstrated significant differences in mucosal microbiota between IBS bowel habit subtypes but not between IBS and healthy controls. In addition, the study reported gut microbiota is associated with abdominal pain in patients with IBS.
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Affiliation(s)
- Charlene Choo
- 1David Geffen School of Medicine, University of
California, Los Angeles, California
| | - Swapna Mahurkar-Joshi
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Tien S. Dong
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Adrienne Lenhart
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Venu Lagishetty
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Jonathan P. Jacobs
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California,4Division of Gastroenterology, Hepatology and Parenteral Nutrition,
Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jennifer S. Labus
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Nancee Jaffe
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Emeran A. Mayer
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Lin Chang
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
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27
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Koyande N, Gangopadhyay M, Thatikonda S, Rengan AK. The role of gut microbiota in the development of colorectal cancer: a review. Int J Colorectal Dis 2022; 37:1509-1523. [PMID: 35704091 DOI: 10.1007/s00384-022-04192-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/21/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE Colorectal cancer (CRC) is the cancer of the colon and rectum. Recent research has found a link between CRC and human gut microbiota. This review explores the effect of gut microbiota on colorectal carcinogenesis and the development of chemoresistance. METHODS A literature overview was performed to identify the gut microbiota species that showed altered abundance in CRC patients and the mechanisms by which some of them aid in the development of chemoresistance. RESULTS Types of gut microbiota present and methods of analyzing them were discussed. We observed that numerous microbiota showed altered abundance in CRC patients and could act as a biomarker for CRC diagnosis and treatment. Further, it was demonstrated that microbes also have a role in the development of chemoresistance by mechanisms like immune system activation, drug modification, and autophagy modulation. Finally, the key issue of the growing global problem of antimicrobial resistance and its relationship with CRC was highlighted. CONCLUSION This review discussed the role of gut microbiota dysbiosis on colorectal cancer progression and the development of chemoresistance.
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Affiliation(s)
- Navami Koyande
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Madhusree Gangopadhyay
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Shashidhar Thatikonda
- Department of Civil Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India
| | - Aravind Kumar Rengan
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy- 502284, India.
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28
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Čipčić Paljetak H, Barešić A, Panek M, Perić M, Matijašić M, Lojkić I, Barišić A, Vranešić Bender D, Ljubas Kelečić D, Brinar M, Kalauz M, Miličević M, Grgić D, Turk N, Karas I, Čuković-Čavka S, Krznarić Ž, Verbanac D. Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients. Gut Microbes 2022; 14:2083419. [PMID: 35695669 PMCID: PMC9196785 DOI: 10.1080/19490976.2022.2083419] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at the onset of disease is still scarce. We compared gut microbiota in newly diagnosed, treatment-naïve adult IBD (Crohn's disease (CD) and ulcerative colitis (UC)) to irritable bowel syndrome (IBS) patients and healthy group. Mucosal and fecal microbiota of 49 patients (13 UC, 10 CD, and 26 IBS) before treatment initiation, and fecal microbiota of 12 healthy subjects was characterized by 16S rRNA gene sequencing. Mucosa was sampled at six positions, from terminal ileum to rectum. We demonstrate that mucosal microbiota is spatially homogeneous, cannot be differentiated based on the local inflammation status and yet provides bacterial footprints superior to fecal in discriminating disease phenotypes. IBD groups showed decreased bacterial diversity in mucosa at all taxonomic levels compared to IBS. In CD and UC, Dialister was significantly increased, and expansion of Haemophilus and Propionibacterium characterized UC. Compared to healthy individuals, fecal microbiota of IBD and IBS patients had increased abundance of Proteobacteria, Enterobacteriaceae, in particular. Shift toward reduction of Adlercreutzia and butyrate-producing taxa was found in feces of IBD patients. Microbiota alterations detected in newly diagnosed treatment-naïve adult patients indicate that the microbiota changes are set and detectable at the disease onset and likely have a discerning role in IBD pathophysiology. Our results justify further investigation of the taxa discriminating between disease groups, such as H. parainfluenzae, R. gnavus, Turicibacteriaceae, Dialister, and Adlercreutzia as potential biomarkers of the disease.
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Affiliation(s)
- Hana Čipčić Paljetak
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Zagreb, Croatia,CONTACT Hana Čipčić Paljetak Center for Translational and Clinical Research, University of Zagreb School of Medicine, Šalata 2, Zagreb10000, Croatia
| | - Anja Barešić
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marina Panek
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Mihaela Perić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Mario Matijašić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ivana Lojkić
- Department for Virology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ana Barišić
- Department of Internal Medicine, Unit of Clinical Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia,University of Zagreb School of Medicine, Zagreb, Croatia
| | - Darija Vranešić Bender
- Department of Internal Medicine, Unit of Clinical Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Dina Ljubas Kelečić
- Department of Internal Medicine, Unit of Clinical Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marko Brinar
- University of Zagreb School of Medicine, Zagreb, Croatia,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mirjana Kalauz
- University of Zagreb School of Medicine, Zagreb, Croatia,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Marija Miličević
- University of Zagreb School of Medicine, Zagreb, Croatia,Department of Gastroenterology, Hepatology and Clinical Nutrition, University Hospital Dubrava, Zagreb, Croatia
| | - Dora Grgić
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nikša Turk
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Irena Karas
- Department of Internal Medicine, Unit of Clinical Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Silvija Čuković-Čavka
- University of Zagreb School of Medicine, Zagreb, Croatia,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Željko Krznarić
- Department of Internal Medicine, Unit of Clinical Nutrition, University Hospital Centre Zagreb, Zagreb, Croatia,University of Zagreb School of Medicine, Zagreb, Croatia,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Donatella Verbanac
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Zagreb, Croatia
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29
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Hartmann P. Editorial: The Microbiome in Hepatobiliary and Intestinal Disease. Front Physiol 2022; 13:893074. [PMID: 35492588 PMCID: PMC9044070 DOI: 10.3389/fphys.2022.893074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Phillipp Hartmann
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
- Division of Gastroenterology, Hepatology and Nutrition, Rady Children’s Hospital San Diego, San Diego, CA, United States
- *Correspondence: Phillipp Hartmann,
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30
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Mamieva Z, Poluektova E, Svistushkin V, Sobolev V, Shifrin O, Guarner F, Ivashkin V. Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations? World J Gastroenterol 2022; 28:1204-1219. [PMID: 35431513 PMCID: PMC8968486 DOI: 10.3748/wjg.v28.i12.1204] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder in which recurrent abdominal pain is associated with defecation or a change in bowel habits (constipation, diarrhea, or both), and it is often accompanied by symptoms of abdominal bloating and distension. IBS is an important health care issue because it negatively affects the quality of life of patients and places a considerable financial burden on health care systems. Despite extensive research, the etiology and underlying pathophysiology of IBS remain incompletely understood. Proposed mechanisms involved in its pathogenesis include increased intestinal permeability, changes in the immune system, visceral hypersensitivity, impaired gut motility, and emotional disorders. Recently, accumulating evidence has highlighted the important role of the gut microbiota in the development of IBS. Microbial dysbiosis within the gut is thought to contribute to all aspects of its multifactorial pathogenesis. The last few decades have also seen an increasing interest in the impact of antibiotics on the gut microbiota. Moreover, antibiotics have been suggested to play a role in the development of IBS. Extensive research has established that antibacterial therapy induces remarkable shifts in the bacterial community composition that are quite similar to those observed in IBS. This suggestion is further supported by data from cohort and case-control studies, indicating that antibiotic treatment is associated with an increased risk of IBS. This paper summarizes the main findings on this issue and contributes to a deeper understanding of the link between antibiotic use and the development of IBS.
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Affiliation(s)
- Zarina Mamieva
- Department of Internal Disease Propaedeutics, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Elena Poluektova
- Department of Internal Disease Propaedeutics, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Valery Svistushkin
- Department of Ear, Throat and Nose Diseases, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Vasily Sobolev
- Department of Ear, Throat and Nose Diseases, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Oleg Shifrin
- Department of Internal Disease Propaedeutics, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
| | - Francisco Guarner
- Digestive System Research Unit, Vall d’Hebron Research Institute, Barcelona 08035, Spain
| | - Vladimir Ivashkin
- Department of Internal Disease Propaedeutics, N.V. Sklifosovsky Institute of Clinical Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
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Abstract
Newer 'omics approaches, such as metatranscriptomics and metabolomics, allow functional assessments of the interaction(s) between the gut microbiome and the human host. However, in order to generate meaningful data with these approaches, the method of sample collection is critical. Prior studies have relied on expensive and invasive means toward sample acquisition, such as intestinal biopsy, while other studies have relied on easier methods of collection, such as fecal samples that do not necessarily represent those microbes in contact with the host. In this pilot study, we attempt to characterize a novel, minimally invasive method toward sampling the human microbiome using mucosal cytology brush sampling compared to intestinal gut biopsy samples on 5 healthy participants undergoing routine screening colonoscopy. We compared metatranscriptomic analyses between the two collection methods and identified increased taxonomic evenness and beta diversity in the cytology brush samples and similar community transcriptional profiles between the two methods. Metabolomics assessment demonstrated striking differences between the two methods, implying a difference in bacterial-derived versus human-absorbed metabolites. Put together, this study supports the use of microbiome sampling with cytology brushes, but caution must be exercised when performing metabolomics assessment, as this represents differential metabolite production but not absorption by the host. IMPORTANCE In order to generate meaningful metabolomic and microbiome data, the method of sample collection is critical. This study utilizes and compares two methods for intestinal tissue collection for evaluation of metabolites and microbiomes, finding that using a brush to sample the microbiome provides valuable data. However, for metabolomics assessment, biopsy samples may still be required.
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Vasapolli R, Schulz C, Schweden M, Casèn C, Kirubakaran GT, Kirste KH, Macke L, Link A, Schütte K, Malfertheiner P. Gut microbiota profiles and the role of anti-CdtB and anti-vinculin antibodies in patients with functional gastrointestinal disorders (FGID). Eur J Clin Invest 2021; 51:e13666. [PMID: 34390492 DOI: 10.1111/eci.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/21/2021] [Accepted: 08/08/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Distinct faecal microbiota profiles are reported to be associated with various subtypes of IBS. Circulating antibodies to cytolethal distending toxin B (CdtB) and vinculin are proposed as biomarkers to identify post-infectious IBS. The aim of our study was to analyse serum levels of anti-CdtB and anti-vinculin antibodies in patients with different functional gastrointestinal disorders (FGID) and their correlation with the composition of faecal microbiome. METHODS The study cohort comprised 65 prospectively recruited individuals: 15 with diarrhoea-type-IBS (IBS-D), 13 with constipation-type-IBS (IBS-C), 15 with functional dyspepsia (FD) and 22 healthy controls. FGID subgroups were defined according to Rome III criteria. Serum levels of anti-CdtB and anti-vinculin antibodies were measured by ELISA. Faecal microbiome composition analysis and assessment of dysbiosis were performed by GA-map® Dysbiosis Test. RESULTS Positivity rate either for anti-CdtB or anti-vinculin antibodies was higher in the IBS-C group (76.9%) compared to IBS-D (40.0%), FD (60%) and healthy (63.6%) groups. Dysbiosis was more frequent in subjects positive for anti-CdtB antibodies and in IBS-C patients, who showed an increased amount of opportunistic/pro-inflammatory bacteria and reduced gut protective bacteria. IBS-C patients showed a high inter-individual variation of bacterial communities compared to other FGID subgroups and healthy individuals, whereas microbial profiles of patients with IBS-D and FD were overlapping with those of healthy controls. No bacteria markers showed significant differences between FGID subgroups and healthy controls. CONCLUSION Neither anti-CdtB/anti-vinculin antibodies nor faecal microbial profiles allowed to discriminate between specific FGID subgroups. Dysbiosis was more frequent in patients presenting with anti-CdtB antibodies and in IBS-C patients.
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Affiliation(s)
- Riccardo Vasapolli
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Melanie Schweden
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | | | | | | | - Lukas Macke
- Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Kerstin Schütte
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken, Marienhospital, Osnabrück, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
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Kwon YJ, Kwak HJ, Lee HK, Lim HC, Jung DH. Comparison of bacterial community profiles from large intestine specimens, rectal swabs, and stool samples. Appl Microbiol Biotechnol 2021; 105:9273-9284. [PMID: 34773153 DOI: 10.1007/s00253-021-11650-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/09/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023]
Abstract
The human gastrointestinal tract contains a complex and dynamic population of microorganisms, known as the gut microbiota. Although interest in the role of the gut microbiota in human health has increased in recent years, there remains no standard sampling protocol for analyzing these organisms. Here, we aimed to characterize the microbial composition of distinct segments of the large intestine and to determine whether rectal swabs are suitable for identifying colon microbiota. A total of 100 participants who underwent screening colonoscopy from October 2019 to October 2020 were included in this study. Large intestinal samples (ascending colon, descending colon, sigmoid colon, and rectum) were aspirated by colonoscopy. Rectal swabs were collected before colonoscopy, and stool samples were collected before patients began colonoscopy preparation. All samples were subjected to 16S ribosomal RNA gene sequencing. We identified differences in the number of phylum-level operational taxonomic units among large intestinal samples, rectal swabs, and stool. Five major phyla were detected in all samples (Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria), although their relative abundances varied. Notably, we found that the microbial compositions of rectal swabs were most similar to those of the sigmoid colon and rectum, whereas the microbiota in stool were relatively different than those from the large intestine and rectal swabs. Our results reveal the existence of microbial heterogeneity within different large intestinal compartments and further suggest that rectal swabs are an acceptable and practical tool for gut microbiota analysis. KEY POINTS: • Our findings highlight local microbiome variations within different regions of the large intestine. • Stool samples do not appear to fully recapitulate the gut microbiome. • Our data from a large population-based cohort indicate that rectal swabs can be used to study the gut microbiome.
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Affiliation(s)
- Yu-Jin Kwon
- Department of Family Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea
| | - Hwan Jong Kwak
- MediCloud Corp, 77, Changnyoung-daero 256beon-gil, Yeongtong-gu, Suwon-si, , Gyeonggi-do, Republic of Korea.,Department of Agriculture and Industry, Kangwon National University, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Hyung Ki Lee
- MediCloud Corp, 77, Changnyoung-daero 256beon-gil, Yeongtong-gu, Suwon-si, , Gyeonggi-do, Republic of Korea
| | - Hyun Chul Lim
- Department of Gastroenterology, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea.
| | - Dong-Hyuk Jung
- Department of Family Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, 363, Dongbaekjukjeon-daero, Giheung-gu, Yongin-si, Gyeonggi-do, 16995, Republic of Korea.
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34
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Yang J, Wang P, Liu T, Lin L, Li L, Kou G, Zhou R, Li P, Li Y. Involvement of mucosal flora and enterochromaffin cells of the caecum and descending colon in diarrhoea-predominant irritable bowel syndrome. BMC Microbiol 2021; 21:316. [PMID: 34773967 PMCID: PMC8590216 DOI: 10.1186/s12866-021-02380-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Accumulating evidence supports the pivotal role of intestinal flora in irritable bowel syndrome (IBS). Serotonin synthesis by enterochromaffin (EC) cells is influenced by the gut microbiota and has been reported to have an interaction with IBS. The comparison between the microbiota of the caecal and colonic mucosa in IBS has rarely been studied. The aim of this study was to investigate the relationship between the gut microbiota, EC cells in caecum and descending colon, and diarrhoea-predominant IBS (IBS-D) symptoms. Results A total of 22 IBS-D patients and 22 healthy controls (HCs) were enrolled in our study. Hamilton anxiety (HAM-A) and Hamilton depression (HAM-D) grades increased significantly in IBS-D patients. In addition, the frequency of defecation in IBS-D patients was higher than that in HCs. Among the preponderant bacterial genera, the relative abundance of the Ruminococcus_torques_ group increased in IBS-D patients in caecum samples while Raoultella and Fusobacterium were less abundant. In the descending colon, the abundance of the Ruminococcus_torques_group and Dorea increased in IBS-D patients and Fusobacterium decreased. No difference was observed between the descending colon and caecum in regards to the mucosal-associated microbiota. The number of EC cells in the caecum of IBS-D patients was higher than in HCs and the expression of TPH1 was higher in IBS-D patients both in the caecum and in the descending colon both at the mRNA and protein level. Correlation analysis showed that the Ruminococcus_torques_group was positively associated with HAM-A, HAM-D, EC cell number, IBS-SSS, degree of abdominal pain, frequency of abdominal pain and frequency of defecation. The abundance of Dorea was positively associated with EC cell number, IBS-SSS, HAM-A, HAM-D and frequency of abdominal pain. Conclusions EC cell numbers increased in IBS-D patients and the expression of TPH1 was higher than in HCs. The Ruminococcus torques group and Dorea furthermore seem like promising targets for future research into the treatment of IBS-D patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02380-2.
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Affiliation(s)
- Jingze Yang
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Peng Wang
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Tong Liu
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Lin Lin
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Guanjun Kou
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Ruchen Zhou
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Pan Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China. .,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China. .,Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No. 107, Wenhuaxi Road, Jinan, 250012, Shandong, China.
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35
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Smart pills for gastrointestinal diagnostics and therapy. Adv Drug Deliv Rev 2021; 177:113931. [PMID: 34416311 DOI: 10.1016/j.addr.2021.113931] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022]
Abstract
Ingestible smart pills have the potential to be a powerful clinical tool in the diagnosis and treatment of gastrointestinal disease. Though examples of this technology, such as capsule endoscopy, have been successfully translated from the lab into clinically used products, there are still numerous challenges that need to be overcome. This review gives an overview of the research being done in the area of ingestible smart pills and reports on the technical challenges in this field.
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36
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Abstract
Gut microbiota plays a vital role in human health. The number of microorganisms inhabiting the gastrointestinal (GI) tract has been estimated to exceed 1013. The dominant genera in the human intestine are Firmicutes (more than 180 species of Lactobacillus), Actinobacteria (among others the Bifidobacteriae), Bacteroidetes (the most important is B. fragilis) and Proteobacteria (E. coli, Salmonella, Yersinia, Shigella, Vibrio, Haemophilus, etc.), but the composition of the flora varies individually, as well as in relation to factors such as host genetics, stress, diet, antibiotics and early childhood experiences. Irritable bowel syndrome (IBS) is one of the most common functional gastrointestinal disorders (FGIDs), which has now been renamed disorders of gut-brain interaction, which affect a large number of people worldwide. It is characterized by abdominal pain and altered bowel habits in the absence of obvious anatomic or physiologic abnormalities. It poses a negative economic impact to the global health care system in addition to reducing the quality of life in patients. The pathophysiology of IBS is not fully understood. In IBS subjects gut microbiota relative to healthy controls was observed with an increase in Enterobacteriaceae, Ruminococcus, Clostridium, Dorea species and a decrease of Lactobacillus, Bifidobacterium, and Faecalibacterium species. IBS with diarrhea predominance (IBS-D) IBS with mixed bowel habits (IBS-M) share similarities in the microbial profile. Recent studies suggest that perturbations within "brain-gut-microbiota" axis may lead to IBS development. The aim of this review was to highlight the potential role of gut microbiota on pathophysiological mechanisms underlying IBS.
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Affiliation(s)
- Cristina M Sabo
- Second Department of Internal Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania -
| | - Dan L Dumitrascu
- Second Department of Internal Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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37
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Abstract
Advances in bioinformatics have facilitated investigation of the role of gut microbiota in patients with irritable bowel syndrome (IBS). This article describes the evidence from epidemiologic and clinical observational studies highlighting the link between IBS and gut microbiome by investigating postinfection IBS, small intestinal bacterial overgrowth, and microbial dysbiosis. It highlights the effects of gut microbiota on mechanisms implicated in the pathophysiology of IBS, including gut-brain axis, visceral hypersensitivity, motility, epithelial barrier, and immune activation. In addition, it summarizes the current evidence on microbiome-guided therapies in IBS, including probiotics, antibiotics, diet, and fecal microbiota transplant.
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Affiliation(s)
- Prashant Singh
- Division of Gastroenterology and Hepatology, University of Michigan, MSBR1, Room 6520 B, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.
| | - Anthony Lembo
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Rabb/Rose 1, 330 Brookline Avenue, Boston, MA 02215, USA
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Li J, Zhang R, Ma J, Tang S, Li Y, Li Y, Wan J. Mucosa-Associated Microbial Profile Is Altered in Small Intestinal Bacterial Overgrowth. Front Microbiol 2021; 12:710940. [PMID: 34421869 PMCID: PMC8372370 DOI: 10.3389/fmicb.2021.710940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
The overall gut microbial profile of patients with small intestinal bacterial overgrowth (SIBO) has not been thoroughly investigated. We investigated the microbial communities of mucosal specimens from the duodenum, ileum, sigmoid colon, and feces of patients with and without SIBO, as diagnosed by lactulose breath testing. The bacteria present in the mucosal and fecal samples were identified using 16S rRNA gene sequencing. Further analysis was performed using the linear discriminant analysis (LDA) effect size method, random forest analysis, and receiver operating characteristic analysis. The microbial diversities of the fecal samples were significantly lower than those of the mucosal samples from the duodenum, ileum, and sigmoid colon (P < 0.001, P < 0.001, and P < 0.001, respectively), while the bacterial compositions of the ileac mucosal samples and sigmoid mucosal samples were similar. The bacterial composition of either the fecal or duodenal mucosal samples were significantly different from those of the other three groups (ANOSIM R = 0.305, P = 0.001). The bacterial compositions of the mucosal samples of the duodenum, ileum, and sigmoid colon in the SIBO + subjects were significantly different from those of the SIBO− subjects (ANOSIM P = 0.039, 0.002, and 0.007, respectively). The relative abundances of 7, 18, and 8 genera were significantly different (LDA score > 3) in the mucosal samples of the duodenum, ileum, and sigmoid colon between the SIBO + and SIBO− groups. Four genera (Lactobacillus, Prevotella_1, Dialister, and norank_f__Ruminococcaceae) showed similar changes among the mucosal samples of the duodenum, ileum, and sigmoid colon in the SIBO + subjects. A signature consisting of four genera in the duodenal mucosa, three genera in the ileac mucosa, or six genera in the mucosa of the sigmoid colon exhibited predictive power for SIBO (area under the curve = 0.9, 0.93, and 0.87, respectively). This study provides a comprehensive profile of the gut microbiota in patients with SIBO. Dysbiosis was observed in the mucosa-associated gut microbiome but not in the fecal microbiome of patients with SIBO. Furthermore, we identified mucosa-associated taxa that may be potential biomarkers or therapeutic targets of SIBO. Further investigation is needed on their mechanisms and roles in SIBO.
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Affiliation(s)
- Jia Li
- Medical School of Chinese PLA, Beijing, China.,Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Department of Gastroenterology, The 983th Hospital of Joint Logistic Support Force of PLA, Tianjin, China
| | - Ru Zhang
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Jinxia Ma
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Shuai Tang
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yuan Li
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yi Li
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Jun Wan
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
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Lee KA, Luong MK, Shaw H, Nathan P, Bataille V, Spector TD. The gut microbiome: what the oncologist ought to know. Br J Cancer 2021; 125:1197-1209. [PMID: 34262150 PMCID: PMC8548300 DOI: 10.1038/s41416-021-01467-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/10/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome (GM) has been implicated in a vast number of human pathologies and has become a focus of oncology research over the past 5 years. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation and protection against pathogens. Strong evidence is emerging to support the effects of the GM on the development of some malignancies but also on responses to cancer therapies, most notably, immune checkpoint inhibition. Tools for manipulating the GM including dietary modification, probiotics and faecal microbiota transfer (FMT) are in development. Current understandings of the many complex interrelationships between the GM, cancer, the immune system, nutrition and medication are ultimately based on a combination of short‐term clinical trials and observational studies, paired with an ever-evolving understanding of cancer biology. The next generation of personalised cancer therapies focusses on molecular and phenotypic heterogeneity, tumour evolution and immune status; it is distinctly possible that the GM will become an increasingly central focus amongst them. The aim of this review is to provide clinicians with an overview of microbiome science and our current understanding of the role the GM plays in cancer.
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Affiliation(s)
- K A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK. .,Department of Medical Oncology, Mount Vernon Hospital, Northwood, UK. .,Department of Medical Oncology, The Royal Marsden, London, UK.
| | - M K Luong
- Department of Medical Oncology, Guy's & St Thomas Hospital, London, UK
| | - H Shaw
- Department of Medical Oncology, Mount Vernon Hospital, Northwood, UK.,Early Phase Trial Unit, Department of Medical Oncology, University College London Hospital, London, UK
| | - P Nathan
- Department of Medical Oncology, Mount Vernon Hospital, Northwood, UK
| | - V Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,Department of Dermatology, Mount Vernon Hospital, Northwood, UK
| | - T D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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40
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Naseri K, Dabiri H, Rostami-Nejad M, Yadegar A, Houri H, Olfatifar M, Sadeghi A, Saadati S, Ciacci C, Iovino P, Zali MR. Influence of low FODMAP-gluten free diet on gut microbiota alterations and symptom severity in Iranian patients with irritable bowel syndrome. BMC Gastroenterol 2021. [PMID: 34261437 DOI: 10.1186/s12876-021-01868-5.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Recently, dietary restriction of fermentable carbohydrates (a low-FODMAP diet) in combination with a gluten-free diet (GFD) has been proposed to reduce the symptoms in irritable bowel syndrome (IBS) patients. Different studies reported that IBS has been associated with dysbiosis in the gut microbiota. Additionally, a few studies have reported inflammation in the gastrointestinal (GI) system of adults with IBS. In this study, we aimed to investigate the effects of low FODMAP-gluten free diet (LF-GFD) on clinical symptoms, intestinal microbiota diversity, and fecal calprotectin (FC) level in Iranian patients with IBS. DESIGN In this clinical trial study, 42 patients with IBS (Rome IV criteria) underwent LF-GFD intervention for 6 weeks. Symptoms were assessed using the IBS symptom severity scoring (IBS-SSS), and fecal samples were collected at baseline and after intervention and analyzed by quantitative 16 S rRNA PCR assay. The diversity of gut microbiota compared before and after 6 weeks of dietary intervention. FC was also analyzed by the ELISA method. RESULTS Thirty patients (mean age 37.8 ± 10.7 years) completed the 6-week diet. The IBS-SSS was significantly (P = 0.001) reduced after LF-GFD intervention compared to the baseline. Significant microbial differences before and after intervention were noticed in fecal samples. A significant increase was found in Bacteroidetes, and the Firmicutes to Bacteroidetes (F/B) ratio was significantly (P = 0.001) decreased after the dietary intervention. The value of FC was significantly decreased after 6 weeks of dietary intervention (P = 0.001). CONCLUSIONS Our study suggests that patients with IBS under an LF-GFD had a significant improvement in IBS symptoms severity, with reduced FC level following normalization of their gut microbiota composition. Further rigorous trials are needed to establish a long-term efficacy and safety of this dietary intervention for personalized nutrition in IBS. Clinical Trial Registry Number: IRCT20100524004010N26.
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Affiliation(s)
- Kaveh Naseri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran.
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran
| | - Meysam Olfatifar
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeede Saadati
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Carolina Ciacci
- Gastrointestinal Unit, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, Università di Salerno, Via Allende, 84081, Salerno, Italy
| | - Paola Iovino
- Gastrointestinal Unit, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, Università di Salerno, Via Allende, 84081, Salerno, Italy
| | - Mohammad Reza Zali
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Naseri K, Dabiri H, Rostami-Nejad M, Yadegar A, Houri H, Olfatifar M, Sadeghi A, Saadati S, Ciacci C, Iovino P, Zali MR. Influence of low FODMAP-gluten free diet on gut microbiota alterations and symptom severity in Iranian patients with irritable bowel syndrome. BMC Gastroenterol 2021; 21:292. [PMID: 34261437 PMCID: PMC8278734 DOI: 10.1186/s12876-021-01868-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Recently, dietary restriction of fermentable carbohydrates (a low-FODMAP diet) in combination with a gluten-free diet (GFD) has been proposed to reduce the symptoms in irritable bowel syndrome (IBS) patients. Different studies reported that IBS has been associated with dysbiosis in the gut microbiota. Additionally, a few studies have reported inflammation in the gastrointestinal (GI) system of adults with IBS. In this study, we aimed to investigate the effects of low FODMAP-gluten free diet (LF-GFD) on clinical symptoms, intestinal microbiota diversity, and fecal calprotectin (FC) level in Iranian patients with IBS. DESIGN In this clinical trial study, 42 patients with IBS (Rome IV criteria) underwent LF-GFD intervention for 6 weeks. Symptoms were assessed using the IBS symptom severity scoring (IBS-SSS), and fecal samples were collected at baseline and after intervention and analyzed by quantitative 16 S rRNA PCR assay. The diversity of gut microbiota compared before and after 6 weeks of dietary intervention. FC was also analyzed by the ELISA method. RESULTS Thirty patients (mean age 37.8 ± 10.7 years) completed the 6-week diet. The IBS-SSS was significantly (P = 0.001) reduced after LF-GFD intervention compared to the baseline. Significant microbial differences before and after intervention were noticed in fecal samples. A significant increase was found in Bacteroidetes, and the Firmicutes to Bacteroidetes (F/B) ratio was significantly (P = 0.001) decreased after the dietary intervention. The value of FC was significantly decreased after 6 weeks of dietary intervention (P = 0.001). CONCLUSIONS Our study suggests that patients with IBS under an LF-GFD had a significant improvement in IBS symptoms severity, with reduced FC level following normalization of their gut microbiota composition. Further rigorous trials are needed to establish a long-term efficacy and safety of this dietary intervention for personalized nutrition in IBS. Clinical Trial Registry Number: IRCT20100524004010N26.
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Affiliation(s)
- Kaveh Naseri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran.
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran
| | - Meysam Olfatifar
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeede Saadati
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Carolina Ciacci
- Gastrointestinal Unit, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, Università di Salerno, Via Allende, 84081, Salerno, Italy
| | - Paola Iovino
- Gastrointestinal Unit, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, Università di Salerno, Via Allende, 84081, Salerno, Italy
| | - Mohammad Reza Zali
- Celiac Disease Department, Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Yang Z, Xu F, Li H, He Y. Beyond samples: A metric revealing more connections of gut microbiota between individuals. Comput Struct Biotechnol J 2021; 19:3930-3937. [PMID: 34377361 PMCID: PMC8319210 DOI: 10.1016/j.csbj.2021.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 10/31/2022] Open
Abstract
Studies of gut microbiota explore their complicated connections between individuals of different characteristics by applying different metrics to abundance data obtained from fecal samples. Although classic metrics are capable to quantify differences between samples, the microbiome of fecal sample is not a good surrogate for the gut microbiome of individuals because the microbial populations of the distal colon does not adequately represent that of the entire gastrointestinal tract. To overcome the deficiency of classic metrics in which the differences can be measured between the samples analyzed, but not the corresponding populations, we propose a metric for representing composition differences in the gut microbiota of individuals. Our investigation shows this metric outperforms traditional measures for multiple scenarios. For gut microbiota in diverse geographic populations, this metric presents more explainable data variance than others, not only in regular variance analysis but also in principle component analysis and partition analysis of biologic characteristics. With time-series data, the metric further presents a strong correlation with the time interval of serial sampling. Our findings suggest that the metric is robust and powerfully detects the intrinsic variations in gut microbiota. The metric holds promise for revealing more relations between gut microbiota and human health.
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Affiliation(s)
- Zhen Yang
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feng Xu
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hongdou Li
- Obstetrics Gynecology Hospital, The Institute of Reproduction and Developmental Biology, Fudan University, Shanghai, China
| | - Yungang He
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study. Clocks Sleep 2021; 3:387-397. [PMID: 34287254 PMCID: PMC8293063 DOI: 10.3390/clockssleep3030025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6–8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.
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Liu Y, Li W, Yang H, Zhang X, Wang W, Jia S, Xiang B, Wang Y, Miao L, Zhang H, Wang L, Wang Y, Song J, Sun Y, Chai L, Tian X. Leveraging 16S rRNA Microbiome Sequencing Data to Identify Bacterial Signatures for Irritable Bowel Syndrome. Front Cell Infect Microbiol 2021; 11:645951. [PMID: 34178718 PMCID: PMC8231010 DOI: 10.3389/fcimb.2021.645951] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder characterized by abdominal pain or discomfort. Previous studies have illustrated that the gut microbiota might play a critical role in IBS, but the conclusions of these studies, based on various methods, were almost impossible to compare, and reproducible microorganism signatures were still in question. To cope with this problem, previously published 16S rRNA gene sequencing data from 439 fecal samples, including 253 IBS samples and 186 control samples, were collected and processed with a uniform bioinformatic pipeline. Although we found no significant differences in community structures between IBS and healthy controls at the amplicon sequence variants (ASV) level, machine learning (ML) approaches enabled us to discriminate IBS from healthy controls at genus level. Linear discriminant analysis effect size (LEfSe) analysis was subsequently used to seek out 97 biomarkers across all studies. Then, we quantified the standardized mean difference (SMDs) for all significant genera identified by LEfSe and ML approaches. Pooled results showed that the SMDs of nine genera had statistical significance, in which the abundance of Lachnoclostridium, Dorea, Erysipelatoclostridium, Prevotella 9, and Clostridium sensu stricto 1 in IBS were higher, while the dominant abundance genera of healthy controls were Ruminococcaceae UCG-005, Holdemanella, Coprococcus 2, and Eubacterium coprostanoligenes group. In summary, based on six published studies, this study identified nine new microbiome biomarkers of IBS, which might be a basis for understanding the key gut microbes associated with IBS, and could be used as potential targets for microbiome-based diagnostics and therapeutics.
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Affiliation(s)
- Yuxia Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenhui Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongxia Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wenxiu Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Sitong Jia
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Beibei Xiang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Laboratory of Pharmacology of Traditional Chinese Medical Formulae Co-Constructed by the Province-Ministry, Tianjin University of TCM, Tianjin, China
| | - Lin Wang
- Tianjin Zhongxin Pharmaceutical Group Co., Ltd. Le Ren Tang Pharmaceutical Factory, Tianjin, China
| | - Yujing Wang
- Tianjin Zhongxin Pharmaceutical Group Co., Ltd. Le Ren Tang Pharmaceutical Factory, Tianjin, China
| | - Jixiang Song
- Tianjin Zhongxin Pharmaceutical Group Co., Ltd. Le Ren Tang Pharmaceutical Factory, Tianjin, China
| | - Yingjie Sun
- Tianjin Zhongxin Pharmaceutical Group Co., Ltd. Le Ren Tang Pharmaceutical Factory, Tianjin, China
| | - Lijuan Chai
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Laboratory of Pharmacology of Traditional Chinese Medical Formulae Co-Constructed by the Province-Ministry, Tianjin University of TCM, Tianjin, China
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Rogers AE, Hu YJ, Yue Y, Wissel EF, Petit III RA, Jarrett S, Christie J, Read TD. Shiftwork, functional bowel symptoms, and the microbiome. PeerJ 2021; 9:e11406. [PMID: 34026361 PMCID: PMC8121053 DOI: 10.7717/peerj.11406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are about 15 million Americans working full-time on evening, night, or rotating shifts. Between 48% and 81.9% of those working rotating or night shifts report abdominal pain, constipation, diarrhea and other symptoms of functional bowel disorders. The basis for this high prevalence of functional bowel disorders, including irritable bowel syndrome (IBS), among shift workers is unknown. Animal studies, however, suggest that circadian disruption, similar to that in shift workers, may contribute to the development of GI complaints among shift workers by altering the composition and normal diurnal rhythmicity of the resident intestinal microbes. Therefore, the present study was designed to determine if there were differences in (1) composition and diversity of the microbiome of night shift workers compared to day shift workers; and (2) the composition and diversity of the microbiome among shift workers experiencing functional bowel symptoms compared to shift workers who did not experience functional bowel symptoms. METHODS Fifty-one full time staff nurses who worked either 12-hour day or night shifts completed demographic information, and the Rome III IBS module. They also collected two samples of gut microbiota before the beginning and at the end of their last work shift on day 14, using validated field-tested methods consistent with the Human Microbiome Project. After DNA extraction, 16S rRNA sequencing and assignment to the genus level was completed, samples were then compared to determine if there were (1) differences in the diversity and profile of the microbiome by shift type; (2) if there were differences in the microbiome by time of day for collection; and (3) whether there were differences in the diversity and profile of the microbiome of nurses with IBS and those without IBS. RESULTS There were no differences in alpha or beta diversity of gut microbiota when specimens from day and night shift nurses were compared. There were however marginal differences in beta diversity when specimens collected at the beginning and end of the shifts were compared, with seven OTUs being differentially abundant when collected from day shift workers in the evening. There were also three OTUs to be differentially abundant in participants reporting IBS symptoms.
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Affiliation(s)
- Ann E. Rogers
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States of America
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Ye Yue
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, United States of America
| | - Emily F. Wissel
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States of America
| | - Robert A. Petit III
- Investigational Clinical Microbiology Core, Emory University, Atlanta, GA, United States of America
| | - Simone Jarrett
- Einstein Medical Center Philadelphia, Philadelphia, PA, United States of America
| | - Jennifer Christie
- Division of Digestive Diseases, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Timothy D. Read
- Division of Digestive Diseases, Emory School of Medicine, Emory University, Atlanta, GA, United States of America
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Altomare A, Di Rosa C, Imperia E, Emerenziani S, Cicala M, Guarino MPL. Diarrhea Predominant-Irritable Bowel Syndrome (IBS-D): Effects of Different Nutritional Patterns on Intestinal Dysbiosis and Symptoms. Nutrients 2021; 13:1506. [PMID: 33946961 PMCID: PMC8146452 DOI: 10.3390/nu13051506] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Irritable Bowel Syndrome (IBS) is a chronic functional gastrointestinal disorder characterized by abdominal pain associated with defecation or a change in bowel habits. Gut microbiota, which acts as a real organ with well-defined functions, is in a mutualistic relationship with the host, harvesting additional energy and nutrients from the diet and protecting the host from pathogens; specific alterations in its composition seem to play a crucial role in IBS pathophysiology. It is well known that diet can significantly modulate the intestinal microbiota profile but it is less known how different nutritional approach effective in IBS patients, such as the low-FODMAP diet, could be responsible of intestinal microbiota changes, thus influencing the presence of gastrointestinal (GI) symptoms. The aim of this review was to explore the effects of different nutritional protocols (e.g., traditional nutritional advice, low-FODMAP diet, gluten-free diet, etc.) on IBS-D symptoms and on intestinal microbiota variations in both IBS-D patients and healthy subjects. To date, an ideal nutritional protocol does not exist for IBS-D patients but it seems crucial to consider the effect of the different nutritional approaches on the intestinal microbiota composition to better define an efficient strategy to manage this functional disorder.
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Affiliation(s)
- Annamaria Altomare
- Gastroenterology Unit, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; (A.A.); (S.E.); (M.C.); (M.P.L.G.)
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy;
| | - Claudia Di Rosa
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy;
| | - Elena Imperia
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy;
| | - Sara Emerenziani
- Gastroenterology Unit, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; (A.A.); (S.E.); (M.C.); (M.P.L.G.)
| | - Michele Cicala
- Gastroenterology Unit, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; (A.A.); (S.E.); (M.C.); (M.P.L.G.)
| | - Michele Pier Luca Guarino
- Gastroenterology Unit, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy; (A.A.); (S.E.); (M.C.); (M.P.L.G.)
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Shanahan ER, McMaster JJ, Staudacher HM. Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design. J Hum Nutr Diet 2021; 34:631-644. [PMID: 33639033 DOI: 10.1111/jhn.12868] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.
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Affiliation(s)
- Erin R Shanahan
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | | | - Heidi M Staudacher
- IMPACT (The Institute for Mental and Physical Health and Clinical Translation) Food & Mood Centre, Deakin University, Geelong, VIC, Australia
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Fredericks E, Theunissen R, Roux S. Short chain fatty acids and monocarboxylate transporters in irritable bowel syndrome. TURKISH JOURNAL OF GASTROENTEROLOGY 2021; 31:840-847. [PMID: 33625995 DOI: 10.5152/tjg.2020.19856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS Gut microbiota ferments indigestible food that rests in the colon to produce short-chain fatty acids (SCFAs) acetate, propionate, and butyrate. Colonic SCFA stimulate the synthesis of serotonin which is central in irritable bowel syndrome (IBS) pathophysiology. Reduced SCFA have been linked to specific IBS symptoms like colonic hyperalgesia and hypersensitivity. SCFA enter the colonocyte mainly via 2 energy-dependent monocarboxylate transporters, MCT1 (SLC16A1) and SMCT1 (SLC5A8). We investigated specific gut microbiota, SCFA concentrations, and monocarboxylate transporter mRNA expression in patients with IBS. MATERIAL AND METHODS A total of 30 IBS patients-15 constipation-predominant (C-IBS) and 15 diarrhoea-predominant (D-IBS)-and 15 healthy controls were recruited. Bacteroidetes and Bifidobacterium species were analyzed using quantitative polymerase chain reaction (qPCR) on stool samples. SCFA concentrations were determined by gas chromatography/mass spectroscopy of stool samples. Monocarboxylate transporter mRNA was quantified by qPCR on colon biopsy specimens. RESULTS Bacteroides was significantly increased in the D-IBS group compared with the C-IBS group and healthy controls. Bifidobacterium was significantly reduced in both IBS groups. SCFA ratios were altered in both IBS groups with a reduction of all 3 measured SCFA in C-IBS and acetic acid in D-IBS. MCT1 and SMCT1 were significantly reduced in C-IBS and D-IBS. CONCLUSION In agreement with findings of previous studies, the microbiota assessed were significantly altered inferring dysbiosis in IBS. SCFA and their ratios were significantly altered in both IBS groups. SCFA transporters, MCT1 and SMCT1 were significantly reduced in both IBS groups, suggesting reduced colonocyte SCFA transfer. SCFA availability and transfer into the colonocytes may be important in IBS pathogenesis and should be prospectively studied.
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Affiliation(s)
- Ernst Fredericks
- Department of Physiology, Nelson Mandela University School of Science, Port Elizabeth, South Africa
| | - Reza Theunissen
- Department of Physiology, Nelson Mandela University School of Science, Port Elizabeth, South Africa
| | - Saartjie Roux
- Department of Physiology, Nelson Mandela University School of Science, Port Elizabeth, South Africa
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Rogler G, Scharl M, Spalinger M, Yilmaz B, Zaugg M, Hersberger M, Schreiner P, Biedermann L, Herfarth H. Diet and Inflammatory Bowel Disease: What Quality Standards Should Be Applied in Clinical and Laboratory Studies? Mol Nutr Food Res 2021; 65:e2000514. [PMID: 33433954 DOI: 10.1002/mnfr.202000514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/21/2020] [Indexed: 12/11/2022]
Abstract
Many patients suffering from inflammatory bowel disease (IBD) follow restrictive diets, as many respective recommendations circulate. Efforts are made to evaluate and summarize the published information, for example, in a recent consensus manuscript by the International Organization for the Study of IBD (IOIBD). However, the standards that should be applied to make claims about dietary effects are poorly defined. In this manuscript, the scientific basis of recommendations for nutritional interventions in IBD is analyzed. Epidemiological evidence on diet in IBD is always biased by numerous factors, and the number of robust dietary intervention studies is limited due to methodological difficulties. Therefore, animal models are used to test hypotheses with respect to dietary factors and intestinal inflammation. Naturally, animal models have limitations, and knowledge of key characteristics of colitis animal models is crucial to understand their advantages and disadvantages. In recent years the important role of the microbiota for IBD and dietary factors has been discovered. Microbiota data are added to many publications on IBD and nutrition. The quality of those data varies largely. Subsequently, quality standards for microbiota analyses also are discussed. Finally, quality requirements to be applied on recommendations for dietary changes in patients with IBD are suggested.
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Affiliation(s)
- Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich 8091, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich 8091, Switzerland
| | - Marianne Spalinger
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich 8091, Switzerland
| | - Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University Clinic of Visceral Surgery and Medicine, Inselspital, University of Bern, Bern, 3010, Switzerland
| | - Michael Zaugg
- Department of Pharmacology and Department of Anesthesiology and Pain Medicine and Cardiovascular Research Centre, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Martin Hersberger
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Philipp Schreiner
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich 8091, Switzerland
| | - Luc Biedermann
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich 8091, Switzerland
| | - Hans Herfarth
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, 27599-7080, USA
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Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components. J Pers Med 2021; 11:jpm11010035. [PMID: 33429936 PMCID: PMC7827153 DOI: 10.3390/jpm11010035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023] Open
Abstract
The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.
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