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Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C. The interplay between diet and the gut microbiome: implications for health and disease. Nat Rev Microbiol 2024; 22:671-686. [PMID: 39009882 DOI: 10.1038/s41579-024-01068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 07/17/2024]
Abstract
Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies.
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Affiliation(s)
- Fiona C Ross
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Dhrati Patangia
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Cork, Ireland
| | - Ghjuvan Grimaud
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Cork, Ireland
| | - Aonghus Lavelle
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eugene M Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- INFANT Centre, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland.
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2
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Liu C, Ruan F, Chen Z, Han J, Ding X, Han C, Ye L, Yang C, Yu Y, Zuo Z, He C. Phenanthrene-induced hyperuricemia with intestinal barrier damage and the protective role of theabrownin: Modulation by gut microbiota-mediated bile acid metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174923. [PMID: 39047823 DOI: 10.1016/j.scitotenv.2024.174923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/24/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Hyperuricemia is prevalent globally and potentially linked to environmental pollution. As a typical persistent organic pollutant, phenanthrene (Phe) poses threats to human health through biomagnification. Although studies have reported Phe-induced toxicities to multiple organs, its impact on uric acid (UA) metabolism remains unclear. In this study, data mining on NHANES 2001-2016 indicated a positive correlation between Phe exposure and the occurrence of hyperuricemia in population. Subsequently, adolescent Balb/c male mice were orally exposed to Phe at a dosage of 10 mg/kg bw every second day for 7 weeks, resulting in dysfunction of intestinal UA excretion and disruption of the intestinal barrier. Utilizing intestinal organoids, 16S rRNA sequencing of gut microbiota, and targeted metabolomic analysis, we further revealed that an imbalance in bile acid metabolism derived from gut microbiota might mediate the intestinal barrier damage. Additionally, the tea extract theabrownin (TB) effectively improved Phe-induced hyperuricemia and intestinal dysfunction at a dose of 320 mg/kg bw per day. In conclusion, this study demonstrates that Phe exposure is positively associated with hyperuricemia and intestinal damage, which provides new insights into the toxic effects induced by Phe. Furthermore, the present study proposes that supplementation with TB would be a healthy and effective improvement strategy for patients with hyperuricemia and intestinal injury caused by environmental factors.
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Affiliation(s)
- Changqian Liu
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fengkai Ruan
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhiyuan Chen
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianrong Han
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaoyan Ding
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Changshun Han
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lingxiao Ye
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chunyan Yang
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yi Yu
- Department of Nephrology, Fujian Clinical Research Center for Chronic Glomerular Disease, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian 361005, China
| | - Zhenghong Zuo
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Endocrinology, Xiang'an Hospital of Xiamen University, School of Medicine, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Chengyong He
- State Key Laboratory of Cellular Stress Biology, Department of Thoracic Surgery, Xiang'an Hospital of Xiamen University, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Endocrinology, Xiang'an Hospital of Xiamen University, School of Medicine, State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
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3
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Lin J, Liu H, Sun Y, Zou J, Nie Q, Nie S. Arabinoxylan Alleviates Obesity by Regulating Gut Microbiota and Bile Acid Metabolism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39400044 DOI: 10.1021/acs.jafc.4c06392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Overweight and obesity are major and increasingly global public health concern. High intake of dietary fiber is negatively correlated with obesity and obesity-related metabolic diseases. Here, we investigated the impact of arabinoxylan on obesity based on the modification of gut microecology. Arabionxylan reduced body weight and improved glucose metabolism, as well as intestinal barrier function and metabolic endotoxemia in obese mice. Supplementation with arabinoxylan increased the relative abundance of Prevotellaceae_UCG_001, Lachnospiraceae_NK4A136_group, Clostridia_UCG_014, Alistipes, Bacteroides, and Ruminococcus, which was associated with the upregulated 7α-dehydroxylation function and production of secondary bile acids (deoxycholic acid and lithocholic acid). The modification of gut microbiota by arabinoxylan also influenced the production of SCFAs, genistein, daidzein, indolelactic acid, and indoleacetic acid, contributing to the amelioration of obesity. Our study highlights the antiobesity effects of arabinoxylan through the modification of gut microbiota and the production of bioactive metabolites.
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Affiliation(s)
- Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Huiying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yonggan Sun
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Jianqiao Zou
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang 330047, China
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4
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Westerbeke FHM, Attaye I, Rios-Morales M, Nieuwdorp M. Glycaemic sugar metabolism and the gut microbiota: past, present and future. FEBS J 2024. [PMID: 39359099 DOI: 10.1111/febs.17293] [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: 10/18/2023] [Revised: 08/02/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
Non-communicable diseases (NCDs), such as type 2 diabetes (T2D) and metabolic dysfunction-associated fatty liver disease, have reached epidemic proportions worldwide. The global increase in dietary sugar consumption, which is largely attributed to the production and widespread use of cheap alternatives such as high-fructose corn syrup, is a major driving factor of NCDs. Therefore, a comprehensive understanding of sugar metabolism and its impact on host health is imperative to rise to the challenge of reducing NCDs. Notably, fructose appears to exert more pronounced deleterious effects than glucose, as hepatic fructose metabolism induces de novo lipogenesis and insulin resistance through distinct mechanisms. Furthermore, recent studies have demonstrated an intricate relationship between sugar metabolism and the small intestinal microbiota (SIM). In contrast to the beneficial role of colonic microbiota in complex carbohydrate metabolism, sugar metabolism by the SIM appears to be less beneficial to the host as it can generate toxic metabolites. These fermentation products can serve as a substrate for fatty acid synthesis, imposing negative health effects on the host. Nevertheless, due to the challenging accessibility of the small intestine, our knowledge of the SIM and its involvement in sugar metabolism remains limited. This review presents an overview of the current knowledge in this field along with implications for future research, ultimately offering potential therapeutic avenues for addressing NCDs.
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Affiliation(s)
- Florine H M Westerbeke
- Department of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, location AMC, The Netherlands
| | - Ilias Attaye
- Department of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, location AMC, The Netherlands
| | - Melany Rios-Morales
- Department of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, location AMC, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, location AMC, The Netherlands
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Nagpal S, Srivastava SK. Colon or semicolon: gut sampling microdevices for omics insights. NPJ Biofilms Microbiomes 2024; 10:97. [PMID: 39358351 PMCID: PMC11447266 DOI: 10.1038/s41522-024-00536-2] [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: 12/20/2023] [Accepted: 07/19/2024] [Indexed: 10/04/2024] Open
Abstract
Ingestible microdevices represent a breakthrough in non-invasive sampling of the human gastrointestinal (GI) tract. By capturing the native spatiotemporal microbiome and intricate biochemical gradients, these devices allow a non-invasive multi-omic access to the unperturbed host-microbiota crosstalk, immune/nutritional landscapes and gut-organ connections. We present the current progress of GI sampling microdevices towards personalized metabolism and fostering collaboration among clinicians, engineers, and data scientists.
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Affiliation(s)
- Sunil Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sarvesh Kumar Srivastava
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, India.
- Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, India.
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Shay JES, Yilmaz ÖH. Dietary and metabolic effects on intestinal stem cells in health and disease. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00980-7. [PMID: 39358589 DOI: 10.1038/s41575-024-00980-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/05/2024] [Indexed: 10/04/2024]
Abstract
Diet and nutritional metabolites exhibit wide-ranging effects on health and disease partly by altering tissue composition and function. With rapidly rising rates of obesity, there is particular interest in how obesogenic diets influence tissue homeostasis and risk of tumorigenesis; epidemiologically, these diets have a positive correlation with various cancers, including colorectal cancer. The gastrointestinal tract is a highly specialized, continuously renewing tissue with a fundamental role in nutrient uptake and is, in turn, influenced by diet composition and host metabolic state. Intestinal stem cells are found at the base of the intestinal crypt and can generate all mature lineages that comprise the intestinal epithelium and are uniquely influenced by host diet, metabolic by-products and energy dynamics. Similarly, tumour growth and metabolism can also be shaped by nutrient availability and host diet. In this Review, we discuss how different diets and metabolic changes influence intestinal stem cells in homeostatic and pathological conditions, as well as tumorigenesis. We also discuss how dietary changes and composition affect the intestinal epithelium and its surrounding microenvironment.
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Affiliation(s)
- Jessica E S Shay
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ömer H Yilmaz
- Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
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7
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Garbutt P, Cyranka M, Michl J, Maejima Y, Vedovato N, Shimomura K, Swietach P, de Wet H. The release of GLP-1 from gut L cells is inhibited by low extracellular pH. Obesity (Silver Spring) 2024; 32:1819-1824. [PMID: 39238194 DOI: 10.1002/oby.24125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/18/2024] [Accepted: 06/30/2024] [Indexed: 09/07/2024]
Abstract
OBJECTIVE The intestinal luminal pH profile varies from stomach to rectum and becomes disrupted in diseases. However, little is known about the pH dependence of incretin hormone secretion, with most in vitro studies having failed to consider this modulatory factor or having used nonphysiological buffer systems. Here, we report the extracellular pH (pHe) dependence of glucagon-like peptide-1 (GLP-1) exocytosis from L cells. METHODS The pHe dependence of GLP-1 release from GLUTag cells and murine ex vivo primary gut cultures was detected by ELISA. GLP-1 release was measured over a range of pHe under a physiological (CO2/HCO3 -) buffering regime and in its absence (HEPES buffer). The relationship between intracellular pH (pHi) and pHe was mapped given that at least some component of pH sensitivity is likely to be intracellular. RESULTS GLP-1 secretion from L cells was pHe-dependent and stimulated under alkaline conditions. In the absence of glucose or extracellular calcium, secretion remained at a pHe-insensitive baseline. pHi followed changes in pHe, but the relationship was offset to more alkaline levels in the absence of CO2/HCO3 - buffer and became shallower if [Cl-] changes that normally accompany [HCO3 -] changes were compensated iso-osmotically with gluconate. CONCLUSIONS GLP-1 secretion is sensitive to pHe and the buffer present. Exploiting this mechanism therapeutically may benefit patients with obesity.
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Affiliation(s)
- Philippa Garbutt
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Malgorzata Cyranka
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Johanna Michl
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Yuko Maejima
- Department of Bioregulation and Pharmacological Medicine, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Natascia Vedovato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Kenju Shimomura
- Department of Bioregulation and Pharmacological Medicine, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Heidi de Wet
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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8
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Dallavilla T, Galiè S, Sambruni G, Borin S, Fazio N, Fumagalli-Romario U, Manzo T, Nezi L, Schaefer MH. Differences in the molecular organisation of tumours along the colon are linked to interactions within the tumour ecosystem. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167311. [PMID: 38909851 DOI: 10.1016/j.bbadis.2024.167311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 06/25/2024]
Abstract
Tumours exhibit significant heterogeneity in their molecular profiles across patients, largely influenced by the tissue of origin, where certain driver gene mutations are predominantly associated with specific cancer types. Here, we unveil an additional layer of complexity: some cancer types display anatomic location-specific mutation profiles akin to tissue-specificity. To better understand this phenomenon, we concentrate on colon cancer. While prior studies have noted changes of the frequency of molecular alterations along the colon, the underlying reasons and whether those changes occur rather gradual or are distinct between the left and right colon, remain unclear. Developing and leveraging stringent statistical models on molecular data from 522 colorectal tumours from The Cancer Genome Atlas, we reveal disparities in molecular properties between the left and right colon affecting many genes. Interestingly, alterations in genes responsive to environmental cues and properties of the tumour ecosystem, including metabolites which we quantify in a cohort of 27 colorectal cancer patients, exhibit continuous trends along the colon. Employing network methodologies, we uncover close interactions between metabolites and genes, including drivers of colon cancer, showing continuous abundance or alteration profiles. This underscores how anatomic biases in the composition and interactions within the tumour ecosystem help explaining gradients of carcinogenesis along the colon.
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Affiliation(s)
- Tiziano Dallavilla
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Serena Galiè
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Gaia Sambruni
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Simona Borin
- Digestive Surgery, European Institute of Oncology-IRCCS, Milano, Italy
| | - Nicola Fazio
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCS, Milano, Italy
| | | | - Teresa Manzo
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Luigi Nezi
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy.
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9
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Yersin S, Vonaesch P. Small intestinal microbiota: from taxonomic composition to metabolism. Trends Microbiol 2024; 32:970-983. [PMID: 38503579 DOI: 10.1016/j.tim.2024.02.013] [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: 11/30/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024]
Abstract
The small intestinal microbiota (SIM) is essential for gastrointestinal health, influencing digestion, immune modulation, and nutrient metabolism. Unlike the colonic microbiota, the SIM has been poorly characterized due to sampling challenges and ethical considerations. Current evidence suggests that the SIM consists of five core genera and additional segment-specific taxa. These bacteria closely interact with the human host, regulating nutrient absorption and metabolism. Recent work suggests the presence of two forms of small intestinal bacterial overgrowth, one dominated by oral bacteria (SIOBO) and a second dominated by coliform bacteria. Less invasive sampling techniques, omics approaches, and mechanistic studies will allow a more comprehensive understanding of the SIM, paving the way for interventions engineering the SIM towards better health.
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Affiliation(s)
- Simon Yersin
- Department of Fundamental Microbiology, Université de Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, Université de Lausanne, Lausanne, Switzerland.
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10
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Fuchs CD, Simbrunner B, Baumgartner M, Campell C, Reiberger T, Trauner M. Bile acid metabolism and signaling in liver disease. J Hepatol 2024:S0168-8278(24)02572-8. [PMID: 39349254 DOI: 10.1016/j.jhep.2024.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 09/12/2024] [Accepted: 09/17/2024] [Indexed: 10/02/2024]
Abstract
Bile acids (BAs) have signaling functions efficiently regulating their own metabolism and transport as well as key aspects of lipid and glucose homeostasis. BAs shape the gut microbial flora and conversely are metabolized by microbiota. Disruption of BA transport, metabolism and physiological signaling function contribute to the pathogenesis and progression of a wide range of liver diseases including cholestatic disorders and metabolic dysfunction-associated steatotic liver disease (MASLD) as well as hepatocellular and cholangiocellular carcinoma. Additionally, impaired BA signaling may also affect the intestine and kidney, thereby contributing to failure of gut integrity driving the progression and complications of portal hypertension, cholemic nephropathy and the development of extrahepatic malignancies such as colorectal cancer. This review will summarize recent advances in the understanding of BA signaling, metabolism and transport focusing on transcriptional regulation and novel BA-focused therapeutic strategies for cholestatic and metabolic liver diseases.
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Affiliation(s)
- Claudia D Fuchs
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Benedikt Simbrunner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Maximillian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Clarissa Campell
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Reiberger
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.
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11
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Lopez J, McKeithen-Mead S, Shi H, Nguyen TH, Huang KC, Good BH. Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.614587. [PMID: 39386523 PMCID: PMC11463441 DOI: 10.1101/2024.09.27.614587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (~1:100), but a much larger ratio of phage genomes to bacterial genomes (~4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occurs at a low average rate (~0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone, while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.
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12
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Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Signal Transduct Target Ther 2024; 9:237. [PMID: 39307902 PMCID: PMC11418828 DOI: 10.1038/s41392-024-01946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/26/2024] Open
Abstract
The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.
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Affiliation(s)
- Ziqi Ma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Ashraf Yusuf Rangrez
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
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13
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Son M, Laury ML, Stephenson KB, May T, Hendrixson DT, Koroma AS, Ngegbai AS, Song JH, Naskidashvili N, Goo YA, Manary MJ. The Impact of Milk on Gut Permeability, Fecal 16S rRNA Gene Microbiota Profiling, and Fecal Metabolomics in Children with Moderate Malnutrition in Sierra Leone: A Double-Blind, Randomized Controlled Trial. Am J Clin Nutr 2024:S0002-9165(24)00750-0. [PMID: 39307188 DOI: 10.1016/j.ajcnut.2024.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/06/2024] [Accepted: 09/12/2024] [Indexed: 10/11/2024] Open
Abstract
BACKGROUND Bovine milk is a beneficial ingredient in teh treatment of malnutrition. OBJECTIVES Our objectives were to determine the effect of dietary milk protein and milk carbohydrate on the intestinal permeability, fecal 16S rRNA gene configuration, and fecal metabolomics of children with moderate malnutrition. METHODS This was a randomized, double-blind, controlled trial among 413 children with wasting in rural Sierra Leone who received 1 of the following 4 supplementary foods, which differed in sources of protein and carbohydrate: milk protein and milk carbohydrate (MPMC), milk protein and vegetable carbohydrate (MPVC), vegetable protein and milk carbohydrate (VPMC), or a control group consuming entirely vegetable-based food (VPVC). After 4 wk, urine and stool were collected from participants enrolled with mid-upper arm circumference of <12.1 cm. Urine was analyzed for lactulose excretion (%L). Stool samples were subjected to both 16S rRNA gene analysis to assess β-diversity and untargeted metabolomic abundance. RESULTS Among the 386 children who completed permeability testing, the mean difference (95% CI) in %L excretion as compared with VPVC was 0.01 (-0.05, 0.07) for MPMC, 0.05 (-0.01, 0.11) for MPVC, and 0.01 (-0.05, 0.07) for VPMC. Of the 374 children who provided a stool sample that was analyzed, the β-diversity among bacterial taxa was similar between dietary groups (P > 0.05 for all comparisons). No significant differences between dietary groups were seen among the 20 most abundant bacterial taxa. Among the 5769 unique metabolomic features identified, greater flavonoid levels in VPVC were seen. CONCLUSIONS Abnormal intestinal permeability do not improve with 4 wk of supplementary feeding. Fecal rRNA do not differ with consumption of different diets. This trial was registered at clinicaltrials.gov as NCT04216043.
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Affiliation(s)
- Minsoo Son
- Mass Spectrometry Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Marie L Laury
- Genome Technology Access Center, McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Kevin B Stephenson
- Department of Internal Medicine, Washington University, St. Louis, MO, United States
| | - Thaddaeus May
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX, United States
| | - D Taylor Hendrixson
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | | | | | - Jong Hee Song
- Mass Spectrometry Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | | | - Young Ah Goo
- Mass Spectrometry Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, One Children's Place, Saint Louis, MO, United States; Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States.
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14
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Hoffmann SV, O'Shea JP, Galvin P, Jannin V, Griffin BT. State-of-the-art and future perspectives in ingestible remotely controlled smart capsules for drug delivery: A GENEGUT review. Eur J Pharm Sci 2024; 203:106911. [PMID: 39293502 DOI: 10.1016/j.ejps.2024.106911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/06/2024] [Accepted: 09/14/2024] [Indexed: 09/20/2024]
Abstract
An emerging concern globally, particularly in developed countries, is the rising prevalence of Inflammatory Bowel Disease (IBD), such as Crohn's disease. Oral delivery technologies that can release the active therapeutic cargo specifically at selected sites of inflammation offer great promise to maximise treatment outcomes and minimise off-target effects. Therapeutic strategies for IBD have expanded in recent years, with an increasing focus on biologic and nucleic acid-based therapies. Reliable site-specific delivery in the gastrointestinal (GI) tract is particularly crucial for these therapeutics to ensure sufficient concentrations in the targeted cells. Ingestible smart capsules hold great potential for precise drug delivery. Despite previous unsuccessful endeavours to commercialise drug delivery smart capsules, the current rise in demand and recent advancements in component development, manufacturing, and miniaturisation have reignited interest in ingestible devices. Consequently, this review analyses the advancements in various mechanical and electrical components associated with ingestible smart drug delivery capsules. These components include modules for device localisation, actuation and retention within the GI tract, signal transmission, drug release, power supply, and payload storage. Challenges and constraints associated with previous capsule design functionality are presented, followed by a critical outlook on future design considerations to ensure efficient and reliable site-specific delivery for the local treatment of GI disorders.
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Affiliation(s)
- Sophia V Hoffmann
- School of Pharmacy, University College Cork, College Road, Cork, Ireland
| | - Joseph P O'Shea
- School of Pharmacy, University College Cork, College Road, Cork, Ireland
| | - Paul Galvin
- Tyndall National Institute, University College Cork, Cork T12R5CP, Ireland
| | | | - Brendan T Griffin
- School of Pharmacy, University College Cork, College Road, Cork, Ireland.
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15
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Singh V, Choi SD, Mahra K, Son H, Lee H, Lee YJ, Kim ES, Shin JH. Cultured fecal microbial community and its impact as fecal microbiota transplantation treatment in mice gut inflammation. Appl Microbiol Biotechnol 2024; 108:463. [PMID: 39269473 PMCID: PMC11399162 DOI: 10.1007/s00253-024-13295-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/21/2024] [Accepted: 08/25/2024] [Indexed: 09/15/2024]
Abstract
The fecal microbiome is identical to the gut microbial communities and provides an easy access to the gut microbiome. Therefore, fecal microbial transplantation (FMT) strategies have been used to alter dysbiotic gut microbiomes with healthy fecal microbiota, successfully alleviating various metabolic disorders, such as obesity, type 2 diabetes, and inflammatory bowel disease (IBD). However, the success of FMT treatment is donor-dependent and variations in gut microbes cannot be avoided. This problem may be overcome by using a cultured fecal microbiome. In this study, a human fecal microbiome was cultured using five different media; growth in brain heart infusion (BHI) media resulted in the highest microbial community cell count. The microbiome (16S rRNA) data demonstrated that the cultured microbial communities were similar to that of the original fecal sample. Therefore, the BHI-cultured fecal microbiome was selected for cultured FMT (cFMT). Furthermore, a dextran sodium sulfate (DSS)-induced mice-IBD model was used to confirm the impact of cFMT. Results showed that cFMT effectively alleviated IBD-associated symptoms, including improved gut permeability, restoration of the inflamed gut epithelium, decreased expression of pro-inflammatory cytokines (IFN-γ, TNF-α, IL-1, IL-6, IL-12, and IL-17), and increased expression of anti-inflammatory cytokines (IL-4 and IL-10). Thus, study's findings suggest that cFMT can be a potential alternative to nFMT. KEY POINTS: • In vitro fecal microbial communities were grown in a batch culture using five different media. • Fecal microbial transplantation was performed on DSS-treated mice using cultured and normal fecal microbes. • Cultured fecal microbes effectively alleviated IBD-associated symptoms.
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Affiliation(s)
- Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Seung-Dae Choi
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kanika Mahra
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - HyunWoo Son
- Microbalance Co. Ltd, Daegu, Republic of Korea
| | - Hoyul Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea
| | - Yu-Jeong Lee
- Cell & Matrix Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
- Microbalance Co. Ltd, Daegu, Republic of Korea.
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16
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Asar R, Dhindwal P, Ruzzini A. Structural and functional analysis of a bile salt hydrolase from the bison microbiome. J Biol Chem 2024; 300:107769. [PMID: 39276930 DOI: 10.1016/j.jbc.2024.107769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/26/2024] [Indexed: 09/17/2024] Open
Abstract
The bile salt hydrolases (BSHs) are significant constituents of animal microbiomes. An evolving appreciation of their roles in health and disease has established them as targets of pharmacological inhibition. These bacterial enzymes belong to the N-terminal nucleophile superfamily and are best known to catalyze the deconjugation of glycine or taurine from bile salts to release bile acid substrates for transformation and or metabolism in the gastrointestinal tract. Here, we identify and describe the BSH from a common member of the Plains bison microbiome, Arthrobacter citreus (BSHAc). Steady-state kinetic analyses demonstrated that BSHAc is a broad-spectrum hydrolase with a preference for glycine-conjugates and deoxycholic acid (DCA). Second-order rate constants (kcat/KM) for BSHAc-catalyzed reactions of relevant bile salts-glyco- and tauro-conjugates of cholic acid and DCA- varied by ∼30-fold and measured between 1.4 × 105 and 4.3 × 106 M-1s-1. Interestingly, a pan-BSH inhibitor named AAA-10 acted as a slow irreversible inhibitor of BSHAc with a rate of inactivation (kinact) of ∼2 h-1 and a second order rate constant (kinact/KI) of ∼24 M-1s-1 for the process. Structural characterization of BSHAc reacted with AAA-10 showed covalent modification of the N-terminal cysteine nucleophile, providing molecular details for an enzyme-stabilized product formed from this mechanism-based inhibitor's α-fluoromethyl ketone warhead. Structural comparison of the BSHs and BSH:inhibitor complexes highlighted the plasticity of the steroid-binding site, including a flexible loop that is variable across well-studied BSHs.
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Affiliation(s)
- Radwa Asar
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Poonam Dhindwal
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Antonio Ruzzini
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada; Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
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17
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Baquero DP, Medvedeva S, Martin-Gallausiaux C, Pende N, Sartori-Rupp A, Tachon S, Pedron T, Debarbieux L, Borrel G, Gribaldo S, Krupovic M. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nat Commun 2024; 15:7702. [PMID: 39231967 PMCID: PMC11375127 DOI: 10.1038/s41467-024-51946-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024] Open
Abstract
The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Camille Martin-Gallausiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Nika Pende
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
- University of Vienna, Archaea Physiology and Biotechnology Group, Vienna, Austria
| | - Anna Sartori-Rupp
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Stéphane Tachon
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Thierry Pedron
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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18
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Steigert S, Brouwers J, Verbeke K, Vanuytsel T, Augustijns P. Characterization of luminal contents from the fasted human proximal colon. Eur J Pharm Sci 2024; 200:106821. [PMID: 38823599 DOI: 10.1016/j.ejps.2024.106821] [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: 04/05/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/03/2024]
Abstract
To treat colonic diseases more effectively, improved therapies are urgently needed. In this respect, delivering drugs locally to the colon is a key strategy to achieve higher local drug concentrations while minimizing systemic side effects. Understanding the luminal environment is crucial to efficiently develop such targeted therapies and to predict drug disposition in the colon. In this clinical study, we collected colonic contents from an undisturbed fasted proximal colon via colonoscopy and characterized their composition with regard to drug disposition. Colonic pH, osmolality, protein content, bile salts, lipids, phospholipids and short-chain fatty acids were investigated in 10 healthy volunteers (8 male and 2 female, age 19-25). The unique environment of the proximal colon was reflected in the composition of the sampled luminal fluids and the effect of the microbiota could be observed on the pH (median 6.55), the composition of bile salts (majority deconjugated and secondary), and the abundance of short-chain fatty acids. At the same time, an increase in phospholipid concentration, osmolality and total protein content compared to reported ileal values was seen, likely resulting from desiccation. Lipids could only be found in low quantities and mainly in the form of cholesterol and free fatty acids, showing almost complete digestion and absorption by the time luminal contents reach the colon. All characteristics also displayed the considerable intersubject variability found in different regions of the gastrointestinal tract. This study contributes to an improved understanding of the luminal conditions in the proximal colon and facilitates the development of new predictive tools to study colonic drug absorption.
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Affiliation(s)
- Sebastian Steigert
- Drug Delivery and Disposition, KU Leuven, Gasthuisberg O&N II, Herestraat 49 - box 921, 3000 Leuven, Belgium
| | - Joachim Brouwers
- Drug Delivery and Disposition, KU Leuven, Gasthuisberg O&N II, Herestraat 49 - box 921, 3000 Leuven, Belgium
| | - Kristin Verbeke
- Translational Research Center for Gastrointestinal Disorders, TARGID, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Tim Vanuytsel
- Translational Research Center for Gastrointestinal Disorders, TARGID, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Gastroenterology and Hepatology, University Hospitals Leuven campus Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Patrick Augustijns
- Drug Delivery and Disposition, KU Leuven, Gasthuisberg O&N II, Herestraat 49 - box 921, 3000 Leuven, Belgium.
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19
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Byndloss M, Devkota S, Duca F, Hendrik Niess J, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes Care 2024; 47:1491-1508. [PMID: 38996003 PMCID: PMC11362125 DOI: 10.2337/dci24-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 07/14/2024]
Abstract
This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Suzanne Devkota
- Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
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20
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Sellge G, Ockenga J. [Small intestinal bacterial overgrowth (SIBO) - Therapy, nutrition, microbiome]. Dtsch Med Wochenschr 2024; 149:1071-1079. [PMID: 39208859 DOI: 10.1055/a-2205-5794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
SIBO (small intestinal bacterial overgrowth) is defined by bacterial overgrowth or colonization of the small intestine in combination with gastrointestinal symptoms such as bloating, nausea, pain, diarrhoea, malabsorption and food intolerance. SIBO can be caused by various mechanisms such as reduced intestinal motility, altered gastrointestinal anatomy, reduced gastric acid or pancreatic enzyme production, altered bile acid metabolism, or immune defects. Accordingly, SIBO often develops secondary to different underlying diseases.Diet has a fundamental influence on the composition of the intestinal microbiome and is therefore also a potential pathomechanism in SIBO. Furthermore, food intolerances are common in SIBO patients. However, both aspects have so far been insufficiently investigated. Nevertheless, elemental diets, carbohydrate-reduced diets, as well as pre- and probiotics are potential therapy options.This article provides a summary of current knowledge on the pathophysiology, diagnosis and treatment of SIBO, with particular emphasis on the role of nutrition and the microbiome.
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21
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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetologia 2024; 67:1760-1782. [PMID: 38910152 PMCID: PMC11410996 DOI: 10.1007/s00125-024-06198-1] [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: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne Devkota
- Cedars-Sinai Medical Center, Human Microbiome Research Institute, Los Angeles, CA, USA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain.
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
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22
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Ntekas I, De Vlaminck I. Spatial methods for microbiome-host interactions. Nat Biotechnol 2024; 42:1359-1360. [PMID: 37985877 DOI: 10.1038/s41587-023-01996-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Affiliation(s)
- Ioannis Ntekas
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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23
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Zhu J. New Metabolomic Insights Into Cancer. Cancer J 2024; 30:301-306. [PMID: 39312449 PMCID: PMC11424019 DOI: 10.1097/ppo.0000000000000740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
ABSTRACT Cancer has been marked by metabolic irregularities that fuel various aggressive activities such as rapid cell proliferation, evasion of the immune system, and spread to distant organs. Therefore, exploiting cancer metabolism for diagnosis, monitoring, or treatment has been extensively studied in the past couple of decades with various molecular and cellular techniques. More recently, investigating cancer diagnostics and treatments through advanced metabolomics has emerged, and these comprehensive approaches provide a holistic understanding of cancer metabolism, which supported the discovery of metabolic targets relevant across multiple cancer types and the development of more effective treatments. This study offers highlights of new knowledge on cancer metabolism enabled by recent metabolomics studies and their potential applications in aiding cancer research and predicting cancer treatment outcomes. Specifically, we discussed the use of advanced metabolomics in cancer metabolism, tumor microenvironment, and cancer immunotherapy studies to provide valuable insights that can shape future research efforts in the dynamic field of cancer metabolism research.
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24
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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The Gut Microbiota and Diabetes: Research, Translation, and Clinical Applications-2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes 2024; 73:1391-1410. [PMID: 38912690 PMCID: PMC11333376 DOI: 10.2337/dbi24-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarizes the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organized by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: 1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g., genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomization in humans; 2) the highly individualized nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; 3) because single-time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and 4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Suzanne Devkota
- Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
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25
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Lee PJ, Papachristou GI, Speake C, Lacy-Hulbert A. Immune markers of severe acute pancreatitis. Curr Opin Gastroenterol 2024; 40:389-395. [PMID: 38967941 PMCID: PMC11305979 DOI: 10.1097/mog.0000000000001053] [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] [Indexed: 07/06/2024]
Abstract
PURPOSE OF REVIEW Acute pancreatitis is a common acute inflammatory disorder of the pancreas, and its incidence has been increasing worldwide. Approximately 10% of acute pancreatitis progresses to severe acute pancreatitis (SAP), which carries significant morbidity and mortality. Disordered immune response to pancreatic injury is regarded as a key event that mediates systemic injury in SAP. In this article, we review recent developments in immune biomarkers of SAP and future directions for research. RECENT FINDINGS Given the importance of the NLRP3-inflammasome pathway in mediating systemic inflammatory response syndrome and systemic injury, recent studies have investigated associations of SAP with systemic levels of activators of NLRP3, such as the damage associated molecular patterns (DAMPs) for the first time in human SAP. For example, circulating levels of histones, mitochondrial DNAs, and cell free DNAs have been associated with SAP. A panel of mechanistically relevant immune markers (e.g., panel of Angiopoeitin-2, hepatocyte growth factor, interleukin-8 (IL-8), resistin and sTNF-α R1) carried higher predictive accuracies than existing clinical scores and individual immune markers. Of the cytokines with established relevance to SAP pathogenesis, phase 2 trials of immunotherapies, including tumor necrosis factor (TNF)-alpha inhibition and stimulation of IL-10 production, are underway to determine if altering the immunologic response can reduce the severity of acute pancreatitis (AP). SUMMARY Circulating systemic levels of various DAMPs and a panel of immune markers that possibly reflect activities of different pathways that drive SAP appear promising as predictive biomarkers for SAP. But larger multicenter studies are needed for external validation. Studies investigating immune cellular pathways driving SAP using immunophenotyping techniques are scarce. Interdisciplinary efforts are also needed to bring some of the promising biomarkers to the bedside for validation and testing for clinical utility. Studies investigating the role of and characterization of altered gut-lymph and gut-microbiota in severe AP are needed.
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Affiliation(s)
- Peter J Lee
- Division of Gastroenterology, Hepatology, and Nutrition. Ohio State University Wexner Medical Center, Columbus, OH
| | - Georgios I Papachristou
- Division of Gastroenterology, Hepatology, and Nutrition. Ohio State University Wexner Medical Center, Columbus, OH
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Adam Lacy-Hulbert
- Center for Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington
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26
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Marasco G, Savarino EV, Barbara G. The IBS and SIBO dilemma: Here we go again. Dig Liver Dis 2024:S1590-8658(24)00955-1. [PMID: 39218737 DOI: 10.1016/j.dld.2024.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Affiliation(s)
- Giovanni Marasco
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy.
| | - Edoardo Vincenzo Savarino
- Division of Gastroenterology, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Giovanni Barbara
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy
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27
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Chen H, Shi J, Tang C, Xu J, Li B, Wang J, Zhou Y, Yang Y, Yang H, Huang Q, Yu W, Wang H, Wu D, Hu Y, Zhou H, Sun Q, Lu S. CHIKV infection drives shifts in the gastrointestinal microbiome and metabolites in rhesus monkeys. MICROBIOME 2024; 12:161. [PMID: 39223641 PMCID: PMC11367899 DOI: 10.1186/s40168-024-01895-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Many studies have demonstrated the association between intestinal microbiota and joint diseases. The "gut-joint axis" also has potential roles in chikungunya virus (CHIKV) infection. Pro-inflammatory arthritis after CHIKV infection might disrupt host homeostasis and lead to dysbacteriosis. This study investigated the characteristics of fecal and gut microbiota, intestinal metabolites, and the changes in gene regulation of intestinal tissues after CHIKV infection using multi-omics analysis to explore the involvement of gut microbiota in the pathogenesis of CHIKV infection. RESULTS CHIKV infection increases the systemic burden of inflammation in the GI system of infected animals. Moreover, infection-induced alterations in GI microbiota and metabolites may be indirectly involved in the modulation of GI and bone inflammation after CHIKV infection, including the modulation of inflammasomes and interleukin-17 inflammatory cytokine levels. CONCLUSION Our results suggest that the GI tract and its microbes are involved in the modulation of CHIKV infection, which could serve as an indicator for the adjuvant treatment of CHIKV infection. Video Abstract.
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Affiliation(s)
- Hongyu Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Jiandong Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Cong Tang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Jingwen Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Bai Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Junbin Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Yanan Zhou
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Yun Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Hao Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Qing Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Wenhai Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Haixuan Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Daoju Wu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Yunzhang Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China.
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Insect-Borne Infectious Diseases Control & Yunan International Joint Laboratory of Tropical Infectious Diseases of Yunnan Institute of Parasitic Diseases, Puer, Yunnan, 665000, China.
| | - Qingming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China.
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (IMBCAMS&PUMC), 935 Jiaoling Road, Kunming, Yunnan, 650118, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China.
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28
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Wang H, Zheng Y, Yang M, Wang L, Xu Y, You S, Mao N, Fan J, Ren S. Gut microecology: effective targets for natural products to modulate uric acid metabolism. Front Pharmacol 2024; 15:1446776. [PMID: 39263572 PMCID: PMC11387183 DOI: 10.3389/fphar.2024.1446776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Gut microecology,the complex community consisting of microorganisms and their microenvironments in the gastrointestinal tract, plays a vital role in maintaining overall health and regulating various physiological and pathological processes. Recent studies have highlighted the significant impact of gut microecology on the regulation of uric acid metabolism. Natural products, including monomers, extracts, and traditional Chinese medicine formulations derived from natural sources such as plants, animals, and microorganisms, have also been investigated for their potential role in modulating uric acid metabolism. According to research, The stability of gut microecology is a crucial link for natural products to maintain healthy uric acid metabolism and reduce hyperuricemia-related diseases. Herein, we review the recent advanced evidence revealing the bidirectional regulation between gut microecology and uric acid metabolism. And separately summarize the key evidence of natural extracts and herbal formulations in regulating both aspects. In addition,we elucidated the important mechanisms of natural products in regulating uric acid metabolism and secondary diseases through gut microecology, especially by modulating the composition of gut microbiota, gut mucosal barrier, inflammatory response, purine catalyzation, and associated transporters. This review may offer a novel insight into uric acid and its associated disorders management and highlight a perspective for exploring its potential therapeutic drugs from natural products.
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Affiliation(s)
- Hui Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yixuan Zheng
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mengfan Yang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lu Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yao Xu
- Chengdu Medical College, Chengdu, China
| | - Siqi You
- Chengdu Medical College, Chengdu, China
| | - Nan Mao
- Chengdu Medical College, Chengdu, China
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Junming Fan
- Chengdu Medical College, Chengdu, China
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Sichong Ren
- Chengdu Medical College, Chengdu, China
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China
- TCM Preventative Treatment Research Center of Chengdu Medical College, Chengdu, China
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Beekman CN, Penumutchu S, Peterson R, Han G, Belenky M, Hasan MH, Belenky A, Beura LK, Belenky P. Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment. Cell Rep 2024; 43:114572. [PMID: 39116202 DOI: 10.1016/j.celrep.2024.114572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To date, studies have largely focused on the impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a gastrointestinal (GI) tract-wide integrated multiomic approach to show that amoxicillin (AMX) treatment reduces bacterial abundance, bile salt hydrolase activity, and unconjugated bile acids in the small intestine (SI). Losses of fatty acids (FAs) and increases in acylcarnitines in the large intestine (LI) correspond with spatially distinct expansions of Proteobacteria. Parasutterella excrementihominis engage in FA biosynthesis in the SI, while multiple Klebsiella species employ FA oxidation during expansion in the LI. We subsequently demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the LI while also inhibiting the expansion of Proteobacteria during AMX treatment. These results suggest that the depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI tract.
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Affiliation(s)
- Chapman N Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Rachel Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Geongoo Han
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Marina Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Mohammad H Hasan
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Alexei Belenky
- Felicitex Therapeutics Inc., 27 Strathmore Road, Natick, MA 01760, USA
| | - Lalit K Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.
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30
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Sun XW, Li HR, Jin XL, Tang X, Wang DW, Zhang X, Zhang JG. Structural and Functional Differences in Small Intestinal and Fecal Microbiota: 16S rRNA Gene Investigation in Rats. Microorganisms 2024; 12:1764. [PMID: 39338439 PMCID: PMC11434385 DOI: 10.3390/microorganisms12091764] [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: 07/09/2024] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 09/30/2024] Open
Abstract
To compare the differences in floral composition and functions between the two types of microbiota, ileal contents and feces were collected from Sprague Dawley (SD) rats fed in a conventional or specific-pathogen free (SPF) environment and rats fed a high-fat diet (HFD), and the V3-V4 region of the 16S ribosomal ribonucleic acid (rRNA) gene in these rats was then amplified and sequenced. Compared with feces, about 60% of the bacterial genera in the ileum were exclusive, with low abundance (operational taxonomic units (OTUs) < 1000). Of bacteria shared between the ileum and feces, a few genera were highly abundant (dominant), whereas most had low abundance (less dominant). The dominant bacteria differed between the ileum and feces. Ileal bacteria showed greater β-diversity, and the distance between in-group samples was nearer than that between paired ileum-feces samples. Moreover, the ileum shared various biomarkers and functions with feces (p < 0.05). The HFD and SPF conditions had a profound influence on α-diversity and abundance but not on the exclusive/shared features or β-diversity of samples. The present findings suggested that, under conventional circumstances, fecal bacteria can represent approximately 40% of the low abundant ileal bacterial genera and that dominant fecal bacteria failed to represent the ileal dominant flora. Moreover, fecal flora diversity does not reflect β-diversity in the ileum.
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Affiliation(s)
- Xiao-Wei Sun
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hong-Rui Li
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiao-Lei Jin
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiao Tang
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Da-Wen Wang
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiao Zhang
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian-Gang Zhang
- Pathology Institute, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
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31
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Sudo K, Delmas-Eliason A, Soucy S, Barrack KE, Liu J, Balasubramanian A, Shu CJ, James MJ, Hegner CL, Dionne HD, Rodriguez-Palacios A, Krause HM, O'Toole GA, Karpen SJ, Dawson PA, Schultz D, Sundrud MS. Quantifying Forms and Functions of Enterohepatic Bile Acid Pools in Mice. Cell Mol Gastroenterol Hepatol 2024; 18:101392. [PMID: 39179177 DOI: 10.1016/j.jcmgh.2024.101392] [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: 05/01/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUNDS & AIMS Bile acids (BAs) are core gastrointestinal metabolites with dual functions in lipid absorption and cell signaling. BAs circulate between the liver and distal small intestine (i.e., ileum), yet the dynamics through which complex BA pools are absorbed in the ileum and interact with host intestinal cells in vivo remain poorly understood. Because ileal absorption is rate-limiting in determining which BAs in the intestinal lumen gain access to host intestinal cells and receptors, and at what concentrations, we hypothesized that defining the rates and routes of ileal BA absorption in vivo would yield novel insights into the physiological forms and functions of mouse enterohepatic BA pools. METHODS Using ex vivo mass spectrometry, we quantified 88 BA species and metabolites in the intestinal lumen and superior mesenteric vein of individual wild-type mice, and cage-mates lacking the ileal BA transporter, Asbt/Slc10a2. RESULTS Using these data, we calculated that the pool of BAs circulating through ileal tissue (i.e., the ileal BA pool) in fasting C57BL/6J female mice is ∼0.3 μmol/g. Asbt-mediated transport accounted for ∼80% of this pool and amplified size. Passive permeability explained the remaining ∼20% and generated diversity. Compared with wild-type mice, the ileal BA pool in Asbt-deficient mice was ∼5-fold smaller, enriched in secondary BA species and metabolites normally found in the colon, and elicited unique transcriptional responses on addition to exvivo-cultured ileal explants. CONCLUSIONS This study defines quantitative traits of the mouse enterohepatic BA pool and reveals how aberrant BA metabolism can impinge directly on host intestinal physiology.
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Affiliation(s)
- Koichi Sudo
- Center for Digestive Health, Dartmouth Health, Lebanon, New Hampshire
| | - Amber Delmas-Eliason
- Department of Immunology and Microbiology, Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, Florida
| | - Shannon Soucy
- Department of Biomedical Data Science, Geisel School of Medicine, Hanover, New Hampshire
| | - Kaitlyn E Barrack
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire
| | - Jiabao Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Akshaya Balasubramanian
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire
| | | | | | - Courtney L Hegner
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida
| | - Henry D Dionne
- Center for Digestive Health, Dartmouth Health, Lebanon, New Hampshire
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio; University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire
| | - Saul J Karpen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Hepatology, and Nutrition, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia; Stravitz-Sanyal Liver Institute for Liver Disease and Metabolic Health, Virginia Commonwealth University, Richmond, Virginia
| | - Paul A Dawson
- Division of Pediatric Gastroenterology, Department of Pediatrics, Hepatology, and Nutrition, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, Georgia
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire
| | - Mark S Sundrud
- Center for Digestive Health, Dartmouth Health, Lebanon, New Hampshire; Department of Immunology and Microbiology, Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, Florida; Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, New Hampshire; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida; Department of Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire; Dartmouth Cancer Center, Lebanon, New Hampshire.
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32
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Castells-Nobau A, Mayneris-Perxachs J, Fernández-Real JM. Unlocking the mind-gut connection: Impact of human microbiome on cognition. Cell Host Microbe 2024; 32:1248-1263. [PMID: 39146797 DOI: 10.1016/j.chom.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024]
Abstract
This perspective explores the current understanding of the gut microbiota's impact on cognitive function in apparently healthy humans and in individuals with metabolic disease. We discuss how alterations in gut microbiota can influence cognitive processes, focusing not only on bacterial composition but also on often overlooked components of the gut microbiota, such as bacteriophages and eukaryotes, as well as microbial functionality. We examine the mechanisms through which gut microbes might communicate with the central nervous system, highlighting the complexity of these interactions. We provide a comprehensive overview of the emerging field of microbiota-gut-brain interactions and its significance for cognitive health. Additionally, we summarize novel therapeutic strategies designed to promote cognitive resilience and reduce the risk of cognitive disorders, focusing on interventions that target the gut microbiota. An in-depth understanding of the microbiome-brain axis is imperative for developing innovative treatments aimed at improving cognitive health.
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Affiliation(s)
- Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta Hospital, Girona, Spain; Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain; CIBER Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain.
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33
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Baas FS, Brusselaers N, Nagtegaal ID, Engstrand L, Boleij A. Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis. Cell Host Microbe 2024; 32:1235-1247. [PMID: 39146796 DOI: 10.1016/j.chom.2024.07.008] [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: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
The gut microbiota has been recognized as an important determinant in the initiation and progression of colorectal cancer (CRC), with recent studies shining light on the molecular mechanisms that may contribute to the interactions between microbes and the CRC microenvironment. Despite the increasing wealth of associations being established in the field, proving causality remains challenging. Obstacles include the high variability of the microbiome and its context, both across individuals and across time. Additionally, there is a lack of large and representative cohort studies with long-term follow-up and/or appropriate sampling methods for studying the mucosal microbiome. Finally, most studies focus on CRC, whereas interactions between host and bacteria in early events in carcinogenesis remain elusive, reinforced by the heterogeneity of CRC development. Here, we discuss these current most prominent obstacles, the recent developments, and research needs.
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Affiliation(s)
- Floor S Baas
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden; Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden
| | - Annemarie Boleij
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.
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34
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Baars DP, Fondevila MF, Meijnikman AS, Nieuwdorp M. The central role of the gut microbiota in the pathophysiology and management of type 2 diabetes. Cell Host Microbe 2024; 32:1280-1300. [PMID: 39146799 DOI: 10.1016/j.chom.2024.07.017] [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: 06/17/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
The inhabitants of our intestines, collectively called the gut microbiome, comprise fungi, viruses, and bacterial strains. These microorganisms are involved in the fermentation of dietary compounds and the regulation of our adaptive and innate immune systems. Less known is the reciprocal interaction between the gut microbiota and type 2 diabetes mellitus (T2DM), as well as their role in modifying therapies to reduce associated morbidity and mortality. In this review, we aim to discuss the existing literature on gut microbial strains and their diet-derived metabolites involved in T2DM. We also explore the potential diagnostics and therapeutic avenues the gut microbiota presents for targeted T2DM management. Personalized treatment plans, driven by diet and medication based on the patient's microbiome and clinical markers, could optimize therapy.
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Affiliation(s)
- Daniel P Baars
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Marcos F Fondevila
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abraham S Meijnikman
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands; Diabetes Center Amsterdam, Amsterdam, the Netherlands.
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Jyotsna, Sarkar B, Yadav M, Deka A, Markandey M, Sanyal P, Nagarajan P, Gaikward N, Ahuja V, Mohanty D, Basak S, Gokhale RS. A hepatocyte-specific transcriptional program driven by Rela and Stat3 exacerbates experimental colitis in mice by modulating bile synthesis. eLife 2024; 12:RP93273. [PMID: 39137024 PMCID: PMC11321761 DOI: 10.7554/elife.93273] [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] [Indexed: 08/15/2024] Open
Abstract
Hepatic factors secreted by the liver promote homeostasis and are pivotal for maintaining the liver-gut axis. Bile acid metabolism is one such example wherein, bile acid synthesis occurs in the liver and its biotransformation happens in the intestine. Dysfunctional interactions between the liver and the intestine stimulate varied pathological outcomes through its bidirectional portal communication. Indeed, aberrant bile acid metabolism has been reported in inflammatory bowel disease (IBD). However, the molecular mechanisms underlying these crosstalks that perpetuate intestinal permeability and inflammation remain obscure. Here, we identify a novel hepatic gene program regulated by Rela and Stat3 that accentuates the inflammation in an acute experimental colitis model. Hepatocyte-specific ablation of Rela and Stat3 reduces the levels of primary bile acids in both the liver and the gut and shows a restricted colitogenic phenotype. On supplementation of chenodeoxycholic acid (CDCA), knock-out mice exhibit enhanced colitis-induced alterations. This study provides persuasive evidence for the development of multi-organ strategies for treating IBD and identifies a hepatocyte-specific Rela-Stat3 network as a promising therapeutic target.
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Affiliation(s)
- Jyotsna
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Binayak Sarkar
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Mohit Yadav
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Alvina Deka
- System Immunology Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Manasvini Markandey
- Department of GastroEnterology, All India Institute of Medical SciencesNew DelhiIndia
| | | | - Perumal Nagarajan
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
| | | | - Vineet Ahuja
- Department of GastroEnterology, All India Institute of Medical SciencesNew DelhiIndia
| | - Debasisa Mohanty
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Soumen Basak
- System Immunology Laboratory, National Institute of ImmunologyNew DelhiIndia
| | - Rajesh S Gokhale
- Immunometabolism Laboratory, National Institute of ImmunologyNew DelhiIndia
- Department of Biology, Indian Institute of Science Education and ResearchPashanIndia
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Yin XF, Ye T, Chen HL, Liu J, Mu XF, Li H, Wang J, Hu YJ, Cao H, Kang WQ. The microbiome compositional and functional differences between rectal mucosa and feces. Microbiol Spectr 2024; 12:e0354923. [PMID: 38916335 PMCID: PMC11302734 DOI: 10.1128/spectrum.03549-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population. IMPORTANCE This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.
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Affiliation(s)
- Xiao-Fei Yin
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Taoyu Ye
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Han-Lin Chen
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Junyan Liu
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Xue-Feng Mu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hao Li
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
| | - Jun Wang
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Yuan-Jia Hu
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Hongzhi Cao
- iCarbonX(zhuhai) Company Limited, Zhuhai, China
- Shenzhen Digital Life Institute, Shenzhen, China
- Department of Digital Health, South China Hospital of Shenzhen University, Shenzhen, China
| | - Wen-Quan Kang
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
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Liang C, Zhuang C, Cheng C, Bai J, Wu Y, Li X, Yang J, Li B, Fu W, Zhu Q, Lv J, Tan Y, Kumar Manthari R, Zhao Y, Wang J, Zhang J. Fluoride induces hepatointestinal damage and vitamin B 2 mitigation by regulating IL-17A and Bifidobacterium in ileum. J Adv Res 2024:S2090-1232(24)00317-5. [PMID: 39097090 DOI: 10.1016/j.jare.2024.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/31/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024] Open
Abstract
INTRODUCTION Fluorosis is a global public health disease affecting more than 50 countries and 500 million people. Excessive fluoride damages the liver and intestines, yet the mechanisms and therapeutic approaches remain unclear. OBJECTIVES To explore the mechanisms by which fluoride-induced intestinal-hepatic damage and vitamin B2 alleviation. METHODS Fluoride and/or vitamin B2-treated IL-17A knockout and wild-type mouse models were established, the morphological and functional changes of liver and gut, total bile acid biosynthesis, metabolism, transport, and regulation of FXR-FGF15 signaling pathways were evaluated, the ileal microbiome was further analyzed by 16S rDNA sequence. Finally, Bifidobacterium supplementation mouse model was designed and re-examined the above indicators. RESULTS The results demonstrated that fluoride induced hepatointestinal injury and enterohepatic circulation disorder by altering the synthesis, transporters, and FXR-FGF15 pathway regulation of total bile acid. Importantly, the ileum was found to be the most sensitive and fluoride changed ileal microbiome particularly by reducing abundance of Bifidobacterium. While vitamin B2 supplementation attenuated fluoride-induced enterohepatic circulation dysfunction through IL-17A and ileal microbiome, Bifidobacterium supplementation also reversed fluoride-induced hepatointestinal injury. CONCLUSION Fluoride induces morphological and functional impairment of liver and gut tissues, as well as enterohepatic circulation disorder by altering total bile acid (TBA) synthesis, transporters, and FXR-FGF15 signaling regulation. Vitamin B2 attenuated fluoride-induced enterohepatic circulation disorder through IL-17A knockout and ileal microbiome regulation. The ileum was found to be the most sensitive to fluoride, leading to changes in ileal microbiome, particularly the reduction of Bifidobacterium. Furthermore, Bifidobacterium supplementation reversed fluoride-induced hepatointestinal injury. This study not only elucidates a novel mechanism by which fluoride causes hepatointestinal toxicity, but also provides a new physiological function of vitamin B2, which will be useful in the therapy of fluorosis and other hepatoenterological diseases.
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Affiliation(s)
- Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Cuicui Zhuang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Chenkai Cheng
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Jian Bai
- College of Life Science, Lv Liang University, Lishi, Shanxi 033001, PR China
| | - Yue Wu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Xiang Li
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Jie Yang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Bohui Li
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Weixiang Fu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Qianlong Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Jiawei Lv
- College of Animal Science, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Yanjia Tan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Ram Kumar Manthari
- Department of Biotechnology, GITAM Institute of Science, Gandhi Institute of Technology and Management, Visakhapatnam 530045, Andhra Pradesh, India
| | - Yangfei Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Jundong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Jianhai Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China.
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Sinha AK, Laursen MF, Licht TR. Regulation of microbial gene expression: the key to understanding our gut microbiome. Trends Microbiol 2024:S0966-842X(24)00175-6. [PMID: 39095208 DOI: 10.1016/j.tim.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Abstract
During the past two decades, gut microbiome studies have established the significant impact of the gut microbiota and its metabolites on host health. However, the molecular mechanisms governing the production of microbial metabolites in the gut environment remain insufficiently investigated and thus are poorly understood. Here, we propose that an enhanced understanding of gut microbial gene regulation, which is responsive to dietary components and gut environmental conditions, is needed in the research field and essential for our ability to effectively promote host health and prevent diseases through interventions targeting the gut microbiome.
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Affiliation(s)
- Anurag Kumar Sinha
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
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Luo Z, Zhou W, Xie T, Xu W, Shi C, Xiao Z, Si Y, Ma Y, Ren Q, Di L, Shan J. The role of botanical triterpenoids and steroids in bile acid metabolism, transport, and signaling: Pharmacological and toxicological implications. Acta Pharm Sin B 2024; 14:3385-3415. [PMID: 39220868 PMCID: PMC11365449 DOI: 10.1016/j.apsb.2024.04.027] [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: 12/22/2023] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 09/04/2024] Open
Abstract
Bile acids (BAs) are synthesized by the host liver from cholesterol and are delivered to the intestine, where they undergo further metabolism by gut microbes and circulate between the liver and intestines through various transporters. They serve to emulsify dietary lipids and act as signaling molecules, regulating the host's metabolism and immune homeostasis through specific receptors. Therefore, disruptions in BA metabolism, transport, and signaling are closely associated with cholestasis, metabolic disorders, autoimmune diseases, and others. Botanical triterpenoids and steroids share structural similarities with BAs, and they have been found to modulate BA metabolism, transport, and signaling, potentially exerting pharmacological or toxicological effects. Here, we have updated the research progress on BA, with a particular emphasis on new-found microbial BAs. Additionally, the latest advancements in targeting BA metabolism and signaling for disease treatment are highlighted. Subsequently, the roles of botanical triterpenoids in BA metabolism, transport, and signaling are examined, analyzing their potential pharmacological, toxicological, or drug interaction effects through these mechanisms. Finally, a research paradigm is proposed that utilizes the gut microbiota as a link to interpret the role of these important natural products in BA signaling.
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Affiliation(s)
- Zichen Luo
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wei Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Tong Xie
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weichen Xu
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chen Shi
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zihan Xiao
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Si
- Jiangsu CM Clinical Medicine Innovation Center for Obstetrics, Gynecology, and Reproduction, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210001, China
| | - Yan Ma
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qingling Ren
- Jiangsu CM Clinical Medicine Innovation Center for Obstetrics, Gynecology, and Reproduction, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210001, China
| | - Liuqing Di
- Jiangsu Engineering Research Center for Efficient Delivery System of TCM, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjun Shan
- Medical Metabolomics Center, Institute of Pediatrics, Jiangsu Key Laboratory of Children’s Health and Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
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40
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Stachowska E, Gudan A, Mańkowska-Wierzbicka D, Liebe R, Krawczyk M. Dysbiosis and nutrition in steatotic liver disease: addressing the unrecognized small intestinal bacterial overgrowth (SIBO) challenge. Intern Emerg Med 2024; 19:1229-1234. [PMID: 38499938 DOI: 10.1007/s11739-024-03533-7] [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: 09/25/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024]
Abstract
Steatotic liver disease (SLD) is characterized by hepatic fat accumulation, potentially causing major consequences such as liver decompensation. Currently, we lack medications for the treatment of SLD. Therapeutic recommendations for patients include a hypocaloric diet, weight loss, and physical activity. In particular, the Mediterranean diet is frequently recommended. However, this diet might exacerbate intestinal problems in a subset of patients with coexisting small intestinal bacterial overgrowth (SIBO). Previous studies have reported that SIBO is more predominant in patients with fatty liver than in healthy individuals. Both our research and the findings of others have highlighted a challenge related to nutritional therapy in patients with fatty liver who also suffer from SIBO inasmuch as SIBO induces several phenomena (like bloating or abdominal pain) that can adversely affect patients' quality of life and might be exacerbated by the Mediterranean diet. This may lower their adherence to the intervention. As a solution, we suggest introducing additional diagnostics (e.g., breath test) in patients with SLD who complain of SIBO-like symptoms. The next step is to modify their diets temporarily starting with several weeks of "elimination and sanitation." This would involve restricting products rich in fermentable sugars and polyols, while simultaneously treating the bacterial overgrowth. In summary, while the hypocaloric Mediterranean diet is beneficial for patients with fatty liver, those with coexisting SIBO may experience exacerbated symptoms. It is vital to consider additional diagnostics and dietary modifications for this subset of patients to address both liver and intestinal health concurrently.
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Affiliation(s)
- Ewa Stachowska
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, Broniewskiego 24, 71-460, Szczecin, Poland.
| | - Anna Gudan
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University, Broniewskiego 24, 71-460, Szczecin, Poland
| | - Dorota Mańkowska-Wierzbicka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Roman Liebe
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University, Magdeburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
- Laboratory of Metabolic Liver Diseases, Center for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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41
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Adolph TE, Tilg H. Western diets and chronic diseases. Nat Med 2024; 30:2133-2147. [PMID: 39085420 DOI: 10.1038/s41591-024-03165-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024]
Abstract
'Westernization', which incorporates industrial, cultural and dietary trends, has paralleled the rise of noncommunicable diseases across the globe. Today, the Western-style diet emerges as a key stimulus for gut microbial vulnerability, chronic inflammation and chronic diseases, affecting mainly the cardiovascular system, systemic metabolism and the gut. Here we review the diet of modern times and evaluate the threat it poses for human health by summarizing recent epidemiological, translational and clinical studies. We discuss the links between diet and disease in the context of obesity and type 2 diabetes, cardiovascular diseases, gut and liver diseases and solid malignancies. We collectively interpret the evidence and its limitations and discuss future challenges and strategies to overcome these. We argue that healthcare professionals and societies must react today to the detrimental effects of the Western diet to bring about sustainable change and improved outcomes in the future.
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Affiliation(s)
- Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria.
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42
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Carmody RN, Varady K, Turnbaugh PJ. Digesting the complex metabolic effects of diet on the host and microbiome. Cell 2024; 187:3857-3876. [PMID: 39059362 PMCID: PMC11309583 DOI: 10.1016/j.cell.2024.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/08/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
The past 50 years of interdisciplinary research in humans and model organisms has delivered unprecedented insights into the mechanisms through which diet affects energy balance. However, translating these results to prevent and treat obesity and its associated diseases remains challenging. Given the vast scope of this literature, we focus this Review on recent conceptual advances in molecular nutrition targeting the management of energy balance, including emerging dietary and pharmaceutical interventions and their interactions with the human gut microbiome. Notably, multiple current dietary patterns of interest embrace moderate-to-high fat intake or prioritize the timing of eating over macronutrient intake. Furthermore, the rapid expansion of microbiome research findings has complicated multiple longstanding tenets of nutrition while also providing new opportunities for intervention. Continued progress promises more precise and reliable dietary recommendations that leverage our growing knowledge of the microbiome, the changing landscape of clinical interventions, and our molecular understanding of human biology.
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Affiliation(s)
- Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Krista Varady
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, IL, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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43
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Wang R, Wang C, Chen P, Qi H, Zhang J. Oxidised rice bran oil induced oxidative stress and apoptosis in IPEC-J2 cells via the Nrf2 signalling pathway. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 39037063 DOI: 10.1111/jpn.14025] [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: 11/06/2023] [Revised: 12/05/2023] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
Rice bran oil is a type of rice oil made by leaching or pressing during rice processing and has a high absorption rate after consumption. When oxidative rancidity occurs, it may cause oxidative stress (OS) and affect intestinal function. Meanwhile, the toxic effects of oxidised rice bran oil have been less well studied in pigs. Therefore, the IPEC-J2 cells model was chosen to explore the regulatory mechanisms of oxidised rice bran oil on OS and apoptosis. Oxidised rice bran oil extract treatment (OR) significantly decreased the viability of IPEC-J2 cells. The results showed that OR significantly elevated apoptosis and reactive oxygen species levels and promoted the expression of pro-apoptotic gene Caspase-3 messenger RNA levels. The activation of Nrf2 signalling pathway by OR decreased the cellular antioxidant capacity. This was further evidenced by the expression of kelch-like ECH-associated protein 1, heme oxygenase 1, NADH: quinone oxidoreductase 1, superoxide dismutase 2 and heat shock 70 kDa protein genes and proteins were all downregulated. In conclusion, our results suggested that oxidised rice bran oil induced damage in IPEC-J2 cells through the Nrf2 signalling pathway.
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Affiliation(s)
- Ruqi Wang
- Institute of Food Quality and Nutrition, Academy of National Food and Strategic Reserves Administration, Beijing, People's Republic of China
- Jilin Provincial Key Laboratory of Livestock and Poultry Feed and Feeding in the Northeastern Frigid Area, College of Animal Sciences, Jilin University, Changchun, People's Republic of China
| | - Chuanqi Wang
- Jilin Provincial Key Laboratory of Livestock and Poultry Feed and Feeding in the Northeastern Frigid Area, College of Animal Sciences, Jilin University, Changchun, People's Republic of China
| | - Peide Chen
- Institute of Food Quality and Nutrition, Academy of National Food and Strategic Reserves Administration, Beijing, People's Republic of China
| | - Huiyu Qi
- Jilin Provincial Key Laboratory of Livestock and Poultry Feed and Feeding in the Northeastern Frigid Area, College of Animal Sciences, Jilin University, Changchun, People's Republic of China
| | - Jing Zhang
- Institute of Food Quality and Nutrition, Academy of National Food and Strategic Reserves Administration, Beijing, People's Republic of China
- Jilin Provincial Key Laboratory of Livestock and Poultry Feed and Feeding in the Northeastern Frigid Area, College of Animal Sciences, Jilin University, Changchun, People's Republic of China
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Lee MH, Nuccio SP, Mohanty I, Hagey LR, Dorrestein PC, Chu H, Raffatellu M. How bile acids and the microbiota interact to shape host immunity. Nat Rev Immunol 2024:10.1038/s41577-024-01057-x. [PMID: 39009868 DOI: 10.1038/s41577-024-01057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/17/2024]
Abstract
Bile acids are increasingly appearing in the spotlight owing to their novel impacts on various host processes. Similarly, there is growing attention on members of the microbiota that are responsible for bile acid modifications. With recent advances in technology enabling the discovery and continued identification of microbially conjugated bile acids, the chemical complexity of the bile acid landscape in the body is increasing at a rapid pace. In this Review, we summarize our current understanding of how bile acids and the gut microbiota interact to modulate immune responses during homeostasis and disease, with a particular focus on the gut.
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Affiliation(s)
- Michael H Lee
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Hiutung Chu
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA.
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45
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Grant ET, De Franco H, Desai MS. Non-SCFA microbial metabolites associated with fiber fermentation and host health. Trends Endocrinol Metab 2024:S1043-2760(24)00169-3. [PMID: 38991905 DOI: 10.1016/j.tem.2024.06.009] [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: 04/26/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024]
Abstract
Dietary fiber is degraded by commensal gut microbes to yield host-beneficial short-chain fatty acids (SCFAs), but personalized responses to fiber supplementation highlight a role for other microbial metabolites in shaping host health. In this review we summarize recent findings from dietary fiber intervention studies describing health impacts attributed to microbial metabolites other than SCFAs, particularly secondary bile acids (2°BAs), aromatic amino acid derivatives, neurotransmitters, and B vitamins. We also discuss shifts in microbial metabolism occurring through altered maternal dietary fiber intake and agricultural practices, which warrant further investigation. To optimize the health benefits of dietary fibers, it is essential to survey a range of metabolites and adapt recommendations on a personalized basis, according to the different functional aspects of the microbiome.
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Affiliation(s)
- Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Hélène De Franco
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology, and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
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46
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Li W, Zhan M, Wen Y, Chen Y, Zhang Z, Wang S, Tian D, Tian S. Recent Progress of Oral Functional Nanomaterials for Intestinal Microbiota Regulation. Pharmaceutics 2024; 16:921. [PMID: 39065618 PMCID: PMC11280463 DOI: 10.3390/pharmaceutics16070921] [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: 06/15/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The gut microbiota is closely associated with human health, and alterations in gut microbiota can influence various physiological and pathological activities in the human body. Therefore, microbiota regulation has become an important strategy in current disease treatment, albeit facing numerous challenges. Nanomaterials, owing to their excellent protective properties, drug release capabilities, targeting abilities, and good biocompatibility, have been widely developed and utilized in pharmaceuticals and dietary fields. In recent years, significant progress has been made in research on utilizing nanomaterials to assist in regulating gut microbiota for disease intervention. This review explores the latest advancements in the application of nanomaterials for microbiota regulation and offers insights into the future development of nanomaterials in modulating gut microbiota.
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Affiliation(s)
- Wanneng Li
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Minle Zhan
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Yue Wen
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Yu Chen
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Zhongchao Zhang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Shuhui Wang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China; (W.L.); (Y.W.); (Y.C.); (Z.Z.); (S.W.)
| | - Sidan Tian
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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Tollemeto M, Ursulska S, Welzen PLW, Thamdrup LHE, Malakpour Permlid A, Li Y, Soufi G, Patiño Padial T, Christensen JB, Hagner Nielsen L, van Hest J, Boisen A. Tailored Polymersomes for Enhanced Oral Drug Delivery: pH-Sensitive Systems for Intestinal Delivery of Immunosuppressants. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2403640. [PMID: 38963162 DOI: 10.1002/smll.202403640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/11/2024] [Indexed: 07/05/2024]
Abstract
Ensuring precise drug release at target sites is crucial for effective treatment. Here, pH-responsive nanoparticles for oral administration of mycophenolate mofetil, an alternative therapy for patients with inflammatory bowel disease unresponsive to conventional treatments is developed. However, its oral administration presents challenges due to its low solubility in the small intestine and high solubility and absorption in the stomach. Therefore, this aim is to design a drug delivery system capable of maintaining drug solubility compared to the free drug while delaying absorption from the stomach to the intestine. Successful synthesis and assembly of a block copolymer incorporating a pH-responsive functional group is achieved. Dynamic light scattering indicated a significant change in hydrodynamic size when the pH exceeded 6.5, confirming successful incorporation of the pH-responsive group. Encapsulation and controlled release of mycophenolate mofetil are efficiently demonstrated, with 90% release observed at intestinal pH. In vitro cell culture studies confirmed biocompatibility, showing no toxicity or adverse effects on Caco-2 cells. In vivo oral rat studies indicated reduced drug absorption in the stomach and enhanced absorption in the small intestine with the developed formulation. This research presents a promising drug delivery system with potential applications in the treatment of inflammatory bowel disease.
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Affiliation(s)
- Matteo Tollemeto
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Sintija Ursulska
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Pascal L W Welzen
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Lasse H E Thamdrup
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Atena Malakpour Permlid
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Yudong Li
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Gohar Soufi
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Tania Patiño Padial
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Jørn B Christensen
- Department of Chemistry, University of Copenhagen, Thovaldsensvej 40, Frederiksberg, DK-1871, Denmark
| | - Line Hagner Nielsen
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Jan van Hest
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Anja Boisen
- The Danish National Research Foundation and Villum Foundation's Center IDUN, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
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Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol 2024; 21:493-516. [PMID: 38575682 DOI: 10.1038/s41575-024-00914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/06/2024]
Abstract
Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.
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Affiliation(s)
- Ipsita Mohanty
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lee R Hagey
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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49
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Lin X, Han H, Wang N, Wang C, Qi M, Wang J, Liu G. The Gut Microbial Regulation of Epigenetic Modification from a Metabolic Perspective. Int J Mol Sci 2024; 25:7175. [PMID: 39000282 PMCID: PMC11241073 DOI: 10.3390/ijms25137175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Obesity is a global health challenge that has received increasing attention in contemporary research. The gut microbiota has been implicated in the development of obesity, primarily through its involvement in regulating various host metabolic processes. Recent research suggests that epigenetic modifications may serve as crucial pathways through which the gut microbiota and its metabolites contribute to the pathogenesis of obesity and other metabolic disorders. Hence, understanding the interplay between gut microbiota and epigenetic mechanisms is crucial for elucidating the impact of obesity on the host. This review primarily focuses on the understanding of the relationship between the gut microbiota and its metabolites with epigenetic mechanisms in several obesity-related pathogenic mechanisms, including energy dysregulation, metabolic inflammation, and maternal inheritance. These findings could serve as novel therapeutic targets for probiotics, prebiotics, and fecal microbiota transplantation tools in treating metabolic disruptions. It may also aid in developing therapeutic strategies that modulate the gut microbiota, thereby regulating the metabolic characteristics of obesity.
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Affiliation(s)
- Xingtong Lin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Hui Han
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Nan Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Chengming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Ming Qi
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Jing Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Gang Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (X.L.); (H.H.); (N.W.); (C.W.); (M.Q.)
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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50
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Borrego-Ruiz A, Borrego JJ. Neurodevelopmental Disorders Associated with Gut Microbiome Dysbiosis in Children. CHILDREN (BASEL, SWITZERLAND) 2024; 11:796. [PMID: 39062245 PMCID: PMC11275248 DOI: 10.3390/children11070796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
The formation of the human gut microbiome initiates in utero, and its maturation is established during the first 2-3 years of life. Numerous factors alter the composition of the gut microbiome and its functions, including mode of delivery, early onset of breastfeeding, exposure to antibiotics and chemicals, and maternal stress, among others. The gut microbiome-brain axis refers to the interconnection of biological networks that allow bidirectional communication between the gut microbiome and the brain, involving the nervous, endocrine, and immune systems. Evidence suggests that the gut microbiome and its metabolic byproducts are actively implicated in the regulation of the early brain development. Any disturbance during this stage may adversely affect brain functions, resulting in a variety of neurodevelopmental disorders (NDDs). In the present study, we reviewed recent evidence regarding the impact of the gut microbiome on early brain development, alongside its correlation with significant NDDs, such as autism spectrum disorder, attention-deficit/hyperactivity disorder, Tourette syndrome, cerebral palsy, fetal alcohol spectrum disorders, and genetic NDDs (Rett, Down, Angelman, and Turner syndromes). Understanding changes in the gut microbiome in NDDs may provide new chances for their treatment in the future.
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Affiliation(s)
- Alejandro Borrego-Ruiz
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia (UNED), 28040 Madrid, Spain;
| | - Juan J. Borrego
- Departamento de Microbiología, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA, Plataforma BIONAND, 29010 Málaga, Spain
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