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Palmiotti A, Berk KA, Koehorst M, Hovingh MV, Pranger AT, van Faassen M, de Boer JF, van der Valk ES, van Rossum EFC, Mulder MT, Kuipers F. Reversal of insulin resistance in people with obesity by lifestyle-induced weight loss does not impact the proportion of circulating 12α-hydroxylated bile acids. Diabetes Obes Metab 2024; 26:4019-4029. [PMID: 38957937 DOI: 10.1111/dom.15754] [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: 03/07/2024] [Revised: 06/06/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024]
Abstract
AIM Bile acids (BAs) are implicated in the pathogenesis of several metabolic syndrome-related diseases, including insulin resistance (IR) and type 2 diabetes (T2D). It has been reported that IR and T2D are associated with an increased ratio of 12α/non-12α-hydroxylated BAs in the circulating BA pool. It is, however, unknown whether the improvement of insulin sensitivity inversely affects BA composition in humans. Therefore, we assessed whether lifestyle-induced weight loss induces changes in BA metabolism in people with obesity, with or without T2D, and if these changes are associated with metabolic parameters. MATERIALS AND METHODS Individual BAs and C4 were quantified by ultra-high-performance liquid chromatography-tandem mass spectrometry in plasma samples collected from two cohorts of people with obesity (OB) and with T2D and obesity (T2D), before and after a lifestyle intervention. RESULTS Lifestyle-induced weight loss improved glycaemic control in both cohorts, with plasma BA concentrations not affected by the lifestyle interventions. The ratio of 12α/non-12α-hydroxylated BAs remained unchanged in OB (p = .178) and even slightly increased upon intervention in T2D (p = .0147). Plasma C4 levels were unaffected in OB participants (p = .20) but significantly reduced in T2D after intervention (p = .0003). There were no significant correlations between the ratio of 12α/non-12α-hydroxylated BAs and glucose, insulin, or homeostatic model assessment-IR, nor in plasma triglycerides, low-density lipoprotein cholesterol, lipoprotein (a) in the T2D cohort. CONCLUSIONS Lifestyle-induced weight loss did improve glycaemic control but did not affect BA concentrations. Improvements in insulin sensitivity were not associated with changes in BA parameters in people with obesity, with or without T2D.
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Affiliation(s)
- Anna Palmiotti
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kirsten A Berk
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martijn Koehorst
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Milaine V Hovingh
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alle T Pranger
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Freark de Boer
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eline S van der Valk
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Obesity Centre CGG, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Elisabeth F C van Rossum
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Obesity Centre CGG, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Monique T Mulder
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department for the Biology of Ageing, European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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2
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Attaye I, Witjes JJ, Koopen AM, van der Vossen EW, Zwirs D, Wortelboer K, Collard D, Kemper EM, Winkelmeijer M, Holst JJ, Hazen SL, Kuipers F, Stroes ES, Groen AK, de Vos WM, Nieuwdorp M, Herrema H. Oral Anaerobutyricum soehngenii augments glycemic control in type 2 diabetes. iScience 2024; 27:110455. [PMID: 39139405 PMCID: PMC11321313 DOI: 10.1016/j.isci.2024.110455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/21/2023] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
This randomized, double-blind, placebo-controlled trial investigated the impact of 14-day Anaerobutyricum soehngenii L2-7 supplementation on postprandial glucose levels in 25 White Dutch males with type 2 diabetes (T2D) on stable metformin therapy. The primary endpoint was the effect of A. soehngenii versus placebo on glucose excursions and variability as determined by continuous glucose monitoring. Secondary endpoints were changes in ambulatory 24-h blood pressure, incretins, circulating metabolites and excursions of plasma short-chain fatty acids (SCFAs) and bile acids upon a standardized meal. Results showed that A. soehngenii supplementation for 14 days significantly improved glycemic variability and mean arterial blood pressure, without notable changes in SCFAs, bile acids, incretin levels, or anthropometric parameters as compared to placebo-treated controls. Although well-tolerated and effective in improving glycemic control in the intervention group, further research in larger and more diverse populations is needed to generalize these findings.
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Affiliation(s)
- Ilias Attaye
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, the Netherlands
| | - Julia J. Witjes
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, the Netherlands
| | - Annefleur M. Koopen
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, the Netherlands
| | | | - Diona Zwirs
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Koen Wortelboer
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, the Netherlands
| | - Didier Collard
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Elles Marleen Kemper
- Department of Pharmacy and Clinical Pharmacology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Maaike Winkelmeijer
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jens J. Holst
- NNF Center for Basic Metabolic Research and Department of Biomedical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Folkert Kuipers
- Department of Pediatrics and European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik S.G. Stroes
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Albert K. Groen
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Willem M. de Vos
- Wageningen University, Wageningen, the Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Hilde Herrema
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, the Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam, the Netherlands
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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3
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Wang S, Jiang Y, Che L, Wang RH, Li SC. Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. Nucleic Acids Res 2024; 52:e61. [PMID: 38884260 DOI: 10.1093/nar/gkae515] [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: 09/28/2023] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.
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Affiliation(s)
- Shuai Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Yiqi Jiang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Lijia Che
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Ruo Han Wang
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Shuai Cheng Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
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4
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Zhang S, Zhang H, Zhang C, Wang G, Shi C, Li Z, Gao F, Cui Y, Li M, Yang G. Composition and evolutionary characterization of the gut microbiota in pigs. Int Microbiol 2024; 27:993-1008. [PMID: 37982990 PMCID: PMC11300507 DOI: 10.1007/s10123-023-00449-8] [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: 09/10/2022] [Revised: 10/28/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The intestinal microbiota plays significant role in the physiology and functioning of host organisms. However, there is limited knowledge of the composition and evolution of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3-V4 in the intestinal contents of different pig breeds was analyzed and was compared using high-throughput sequencing. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that potentially influence host phenotypic traits. Overall, these findings suggested that both the composition and functions of the microbiota were closely associated with domestication and the evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.
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Affiliation(s)
- Shuhong Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Huan Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Cheng Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guan Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Chuanxing Shi
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Zhiqiang Li
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Fengyi Gao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yanyan Cui
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Guangli Yang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China.
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5
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Kim N, Ma J, Kim W, Kim J, Belenky P, Lee I. Genome-resolved metagenomics: a game changer for microbiome medicine. Exp Mol Med 2024; 56:1501-1512. [PMID: 38945961 PMCID: PMC11297344 DOI: 10.1038/s12276-024-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 07/02/2024] Open
Abstract
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.
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Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Wonjong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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6
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Yang M, Zheng X, Fan J, Cheng W, Yan T, Lai Y, Zhang N, Lu Y, Qi J, Huo Z, Xu Z, Huang J, Jiao Y, Liu B, Pang R, Zhong X, Huang S, Luo G, Lee G, Jobin C, Eren AM, Chang EB, Wei H, Pan T, Wang X. Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m 6A Epitranscriptome via Bile Acid Metabolism. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307981. [PMID: 38713722 PMCID: PMC11267274 DOI: 10.1002/advs.202307981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Gut microbiota can influence host gene expression and physiology through metabolites. Besides, the presence or absence of gut microbiome can reprogram host transcriptome and epitranscriptome as represented by N6-methyladenosine (m6A), the most abundant mammalian mRNA modification. However, which and how gut microbiota-derived metabolites reprogram host transcriptome and m6A epitranscriptome remain poorly understood. Here, investigation is conducted into how gut microbiota-derived metabolites impact host transcriptome and m6A epitranscriptome using multiple mouse models and multi-omics approaches. Various antibiotics-induced dysbiotic mice are established, followed by fecal microbiota transplantation (FMT) into germ-free mice, and the results show that bile acid metabolism is significantly altered along with the abundance change in bile acid-producing microbiota. Unbalanced gut microbiota and bile acids drastically change the host transcriptome and the m6A epitranscriptome in multiple tissues. Mechanistically, the expression of m6A writer proteins is regulated in animals treated with antibiotics and in cultured cells treated with bile acids, indicating a direct link between bile acid metabolism and m6A biology. Collectively, these results demonstrate that antibiotic-induced gut dysbiosis regulates the landscape of host transcriptome and m6A epitranscriptome via bile acid metabolism pathway. This work provides novel insights into the interplay between microbial metabolites and host gene expression.
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Affiliation(s)
- Meng Yang
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Xiaoqi Zheng
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
- Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou510530China
| | - Jiajun Fan
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Wei Cheng
- College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Tong‐Meng Yan
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and TechnologyTaipaMacau999078China
| | - Yushan Lai
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Nianping Zhang
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Yi Lu
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
- Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou510530China
| | - Jiali Qi
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Zhengyi Huo
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Zihe Xu
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
- Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou510530China
| | - Jia Huang
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Yuting Jiao
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
| | - Biaodi Liu
- MOE Key Laboratory of Gene Function and RegulationState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and HealthState Key Laboratory of Applied Microbiology Southern ChinaInstitute of MicrobiologyGuangdong Academy of SciencesGuangzhou510070China
| | - Xiang Zhong
- College of Animal Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Shi Huang
- Faculty of DentistryThe University of Hong KongHong Kong SARChina
| | - Guan‐Zheng Luo
- MOE Key Laboratory of Gene Function and RegulationState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐sen UniversityGuangzhou510275China
| | - Gina Lee
- Department of Microbiology and Molecular GeneticsChao Family Comprehensive Cancer CenterUniversity of California Irvine School of MedicineIrvineCA92697USA
| | - Christian Jobin
- Department of MedicineUniversity of Florida College of MedicineGainesvilleFL32610USA
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity26129OldenburgGermany
- Institute for Chemistry and Biology of the Marine EnvironmentUniversity of Oldenburg26129OldenburgGermany
| | - Eugene B Chang
- Department of MedicineKnapp Center for Biomedical DiscoveryThe University of Chicago Knapp Center for Biomedical DiscoveryChicagoIL60637USA
| | - Hong Wei
- College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Tao Pan
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIL60637USA
| | - Xiaoyun Wang
- School of Life SciencesSouth China Normal UniversityGuangzhou510631China
- Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou510530China
- University of Chinese Academy of SciencesBeijing100049China
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7
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Zhang Q, Schwarz D, Cheng Y, Sohrabi Y. Unraveling host genetics and microbiome genome crosstalk: a novel therapeutic approach. Trends Mol Med 2024:S1471-4914(24)00165-5. [PMID: 38937208 DOI: 10.1016/j.molmed.2024.06.007] [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: 04/17/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024]
Abstract
The ability of the gut microbiome to adapt to a new environment and utilize a new metabolite or dietary compound by inducing structural variations (SVs) in the genome has an important role in human health. Here, we discuss recent data on host genetic regulation of SV induction and its use as a new therapeutic approach.
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Affiliation(s)
- Qian Zhang
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany
| | - Dennis Schwarz
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany; Institute of Experimental Pathology (ExPat), Center for Molecular Biology of Inflammation (ZMBE), University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany
| | - Yumei Cheng
- Department of Critical Care Medicine, the Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Yahya Sohrabi
- Department of Cardiology I - Coronary and Peripheral Vascular Disease, University Hospital Münster, Westfälische Wilhelms-Universität, Münster, Germany; Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czechia.
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8
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Aydin Ö, Wahlström A, de Jonge PA, Meijnikman AS, Sjöland W, Olsson L, Henricsson M, de Goffau MC, Oonk S, Bruin SC, Acherman YIZ, Marschall HU, Gerdes VEA, Nieuwdorp M, Bäckhed F, Groen AK. An integrated analysis of bile acid metabolism in humans with severe obesity. Hepatology 2024:01515467-990000000-00889. [PMID: 39010331 DOI: 10.1097/hep.0000000000000938] [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: 02/12/2024] [Accepted: 03/26/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND AND AIMS Bile acids (BA) are vital regulators of metabolism. BAs are AQ6 secreted in the small intestine, reabsorbed, and transported back to the liver, where they can modulate metabolic functions. There is a paucity of data regarding the portal BA composition in humans. This study aimed to address this knowledge gap by investigating portal BA composition and the relation with peripheral and fecal BA dynamics in conjunction with the gut microbiome. APPROACH AND RESULTS Thirty-three individuals from the BARIA cohort were included. Portal plasma, peripheral plasma, and feces were collected. BA and C4 levels were measured employing mass spectrometry. FGF19 was measured using ELISA. Gut microbiota composition was determined through metagenomics analysis on stool samples. Considerable diversity in the portal BA composition was observed. The majority (n = 26) of individuals had a 9-fold higher portal than peripheral BA concentration. In contrast, 8 individuals showed lower portal BA concentration compared with peripheral and had higher levels of unconjugated and secondary BA in this compartment, suggesting more distal origin. The altered portal BA profile was associated with altered gut microbiota composition. In particular, taxa within Bacteroides were reduced in abundance in the feces of these individuals. CONCLUSIONS Characterization of the portal BA composition in relation to peripheral and fecal BA increased insight into the dynamics of BA metabolism in individuals with obesity. Peripheral BA composition was much more diverse due to microbial metabolism. About 24% of the portal samples was surprisingly low in total BA; the underlying mechanism requires further exploration.
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Affiliation(s)
- Ömrüm Aydin
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Annika Wahlström
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Patrick A de Jonge
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Abraham S Meijnikman
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Wilhelm Sjöland
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Olsson
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcus Henricsson
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcus C de Goffau
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Stijn Oonk
- Department of Scientific Research, Data Science, Spaarne Gasthuis Hospital, Hoofddorp, the Netherlands
| | - Sjoerd C Bruin
- Department of Bariatric Surgery, Spaarne Gasthuis Hospital, Hoofddorp, the Netherlands
| | - Yair I Z Acherman
- Department of Bariatric Surgery, Spaarne Gasthuis Hospital, Hoofddorp, the Netherlands
| | - Hanns-Ulrich Marschall
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Victor E A Gerdes
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Bariatric Surgery, Spaarne Gasthuis Hospital, Hoofddorp, the Netherlands
- Department of Internal Medicine, Spaarne Gasthuis Hospital, Hoofddorp, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Albert K Groen
- Department of Internal and (Experimental) Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, ACS Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
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9
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Jia W, Li Y, Cheung KCP, Zheng X. Bile acid signaling in the regulation of whole body metabolic and immunological homeostasis. SCIENCE CHINA. LIFE SCIENCES 2024; 67:865-878. [PMID: 37515688 DOI: 10.1007/s11427-023-2353-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/23/2023] [Indexed: 07/31/2023]
Abstract
Bile acids (BAs) play a crucial role in nutrient absorption and act as key regulators of lipid and glucose metabolism and immune homeostasis. Through the enterohepatic circulation, BAs are synthesized, metabolized, and reabsorbed, with a portion entering the vascular circulation and distributing systemically. This allows BAs to interact with receptors in all major organs, leading to organ-organ interactions that regulate both local and global metabolic processes, as well as the immune system. This review focuses on the whole-body effects of BA-mediated metabolic and immunological regulation, including in the brain, heart, liver, intestine, eyes, skin, adipose tissue, and muscle. Targeting BA synthesis and receptor signaling is a promising strategy for the development of novel therapies for various diseases throughout the body.
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Affiliation(s)
- Wei Jia
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Yitao Li
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Kenneth C P Cheung
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiaojiao Zheng
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
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10
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Ridlon JM, Gaskins HR. Another renaissance for bile acid gastrointestinal microbiology. Nat Rev Gastroenterol Hepatol 2024; 21:348-364. [PMID: 38383804 DOI: 10.1038/s41575-024-00896-2] [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: 01/16/2024] [Indexed: 02/23/2024]
Abstract
The field of bile acid microbiology in the gastrointestinal tract is going through a current rebirth after a peak of activity in the late 1970s and early 1980s. This renewed activity is a result of many factors, including the discovery near the turn of the century that bile acids are potent signalling molecules and technological advances in next-generation sequencing, computation, culturomics, gnotobiology, and metabolomics. We describe the current state of the field with particular emphasis on questions that have remained unanswered for many decades in both bile acid synthesis by the host and metabolism by the gut microbiota. Current knowledge of established enzymatic pathways, including bile salt hydrolase, hydroxysteroid dehydrogenases involved in the oxidation and epimerization of bile acid hydroxy groups, the Hylemon-Bjӧrkhem pathway of bile acid C7-dehydroxylation, and the formation of secondary allo-bile acids, is described. We cover aspects of bile acid conjugation and esterification as well as evidence for bile acid C3-dehydroxylation and C12-dehydroxylation that are less well understood but potentially critical for our understanding of bile acid metabolism in the human gut. The physiological consequences of bile acid metabolism for human health, important caveats and cautionary notes on experimental design and interpretation of data reflecting bile acid metabolism are also explored.
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Affiliation(s)
- Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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11
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Liu H, Xiao H, Lin S, Zhou H, Cheng Y, Xie B, Xu D. Effect of gut hormones on bone metabolism and their possible mechanisms in the treatment of osteoporosis. Front Pharmacol 2024; 15:1372399. [PMID: 38725663 PMCID: PMC11079205 DOI: 10.3389/fphar.2024.1372399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/25/2024] [Indexed: 05/12/2024] Open
Abstract
Bone is a highly dynamic organ that changes with the daily circadian rhythm. During the day, bone resorption is suppressed due to eating, while it increases at night. This circadian rhythm of the skeleton is regulated by gut hormones. Until now, gut hormones that have been found to affect skeletal homeostasis include glucagon-like peptide-1 (GLP-1), glucagon-like peptide-2 (GLP-2), glucose-dependent insulinotropic polypeptide (GIP), and peptide YY (PYY), which exerts its effects by binding to its cognate receptors (GLP-1R, GLP-2R, GIPR, and Y1R). Several studies have shown that GLP-1, GLP-2, and GIP all inhibit bone resorption, while GIP also promotes bone formation. Notably, PYY has a strong bone resorption-promoting effect. In addition, gut microbiota (GM) plays an important role in maintaining bone homeostasis. This review outlines the roles of GLP-1, GLP-2, GIP, and PYY in bone metabolism and discusses the roles of gut hormones and the GM in regulating bone homeostasis and their potential mechanisms.
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Affiliation(s)
- Hongyu Liu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Huimin Xiao
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Sufen Lin
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Huan Zhou
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Yizhao Cheng
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
| | - Baocheng Xie
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Department of Pharmacy, The 10th Affiliated Hospital of Southern Medical University (Dongguan People’s Hospital), Dongguan, China
| | - Daohua Xu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Dongguan Key Laboratory of Traditional Chinese Medicine and New Pharmaceutical Development, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Institute of Traditional Chinese Medicine and New Pharmacy Development, Guangdong Medical University, Dongguan, China
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12
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Liu D, Li B, Song P, Jiang F, Zhang T. Captivity Shifts Gut Microbiota Communities in Plateau Zokor ( Eospalax baileyi). Microorganisms 2024; 12:789. [PMID: 38674733 PMCID: PMC11052244 DOI: 10.3390/microorganisms12040789] [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: 03/01/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The gut microbiota in animals is a dynamic ecosystem influenced by both the host itself and the environment it inhabits. It is known that short-term captivity can significantly impact the gut microbiota of plateau zokors, leading to substantial inter-individual variation. However, the specific changes in the assembly process of the gut microbiota in plateau zokors during captivity remain unclear. In this study, we conducted a comparative analysis on the assembly process of the gut microbiota in 22 male plateau zokors from the same location in Qinglin Township, Datong County, Qinghai Province, before (W) and after (L) laboratory rearing. We performed a single-factor correlation network analysis on the top 50 genera with relative abundance in each group. The results revealed that captivity increased the complexity of the gut microbiota in plateau zokors, indicating a higher number of interactions between different microbial species. However, this increase in complexity was accompanied by a decrease in stability, suggesting a higher degree of variability and potential disruption in the microbial community. According to the results of the neutral community model, the gut microbiota of plateau zokors in the W had a higher Nm value (Nm = 48,135) compared to the L (Nm = 39,671), indicating that species dispersal of the gut microbiota was greater in the wild than in captivity. In the wild, the modified stochasticity ratio (MST) was less than 0.5, suggesting that deterministic processes dominated. However, after 15 days of laboratory rearing, the MST became greater than 0.5, indicating a shift toward stochastic processes, and this difference was highly significant (p < 0.001). This differs from research related to aboveground animals. This study provides theoretical support for the application of gut microbiota in subterranean endangered species.
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Affiliation(s)
- Daoxin Liu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China;
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; (B.L.); (P.S.); (F.J.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
| | - Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; (B.L.); (P.S.); (F.J.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; (B.L.); (P.S.); (F.J.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; (B.L.); (P.S.); (F.J.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China; (B.L.); (P.S.); (F.J.)
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China
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13
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Hao Z, Ding X, Wang J. Effects of gut bacteria and their metabolites on gut health of animals. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:223-252. [PMID: 38763528 DOI: 10.1016/bs.aambs.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The intestine tract is a vital site for the body to acquire nutrients, serving as the largest immune organ. Intestinal health is crucial for maintaining a normal physiological state. Abundant microorganisms reside in the intestine, colonized in a symbiotic manner. These microorganisms can generate various metabolites that influence host physiological activities. Microbial metabolites serve as signaling molecules or metabolic substrates in the intestine, and some intestinal microorganisms act as probiotics and promote intestinal health. Researches on host, probiotics, microbial metabolites and their interactions are ongoing. This study reviews the effects of gut bacteria and their metabolites on intestinal health to provide useful references for animal husbandry.
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Affiliation(s)
- Zhuang Hao
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China
| | - Xuedong Ding
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China
| | - Jing Wang
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China.
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14
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Loh JS, Mak WQ, Tan LKS, Ng CX, Chan HH, Yeow SH, Foo JB, Ong YS, How CW, Khaw KY. Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduct Target Ther 2024; 9:37. [PMID: 38360862 PMCID: PMC10869798 DOI: 10.1038/s41392-024-01743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 02/17/2024] Open
Abstract
The human gastrointestinal tract is populated with a diverse microbial community. The vast genetic and metabolic potential of the gut microbiome underpins its ubiquity in nearly every aspect of human biology, including health maintenance, development, aging, and disease. The advent of new sequencing technologies and culture-independent methods has allowed researchers to move beyond correlative studies toward mechanistic explorations to shed light on microbiome-host interactions. Evidence has unveiled the bidirectional communication between the gut microbiome and the central nervous system, referred to as the "microbiota-gut-brain axis". The microbiota-gut-brain axis represents an important regulator of glial functions, making it an actionable target to ameliorate the development and progression of neurodegenerative diseases. In this review, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases. As the gut microbiome provides essential cues to microglia, astrocytes, and oligodendrocytes, we examine the communications between gut microbiota and these glial cells during healthy states and neurodegenerative diseases. Subsequently, we discuss the mechanisms of the microbiota-gut-brain axis in neurodegenerative diseases using a metabolite-centric approach, while also examining the role of gut microbiota-related neurotransmitters and gut hormones. Next, we examine the potential of targeting the intestinal barrier, blood-brain barrier, meninges, and peripheral immune system to counteract glial dysfunction in neurodegeneration. Finally, we conclude by assessing the pre-clinical and clinical evidence of probiotics, prebiotics, and fecal microbiota transplantation in neurodegenerative diseases. A thorough comprehension of the microbiota-gut-brain axis will foster the development of effective therapeutic interventions for the management of neurodegenerative diseases.
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Affiliation(s)
- Jian Sheng Loh
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Wen Qi Mak
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Li Kar Stella Tan
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Hong Hao Chan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Shiau Hueh Yeow
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Jhi Biau Foo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
- Digital Health & Medical Advancements, Taylor's University, 1, Jalan Taylors, Subang Jaya, 47500, Selangor, Malaysia
| | - Yong Sze Ong
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chee Wun How
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kooi Yeong Khaw
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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15
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Kim JW, Hong YK, Kwon OK, Kim SC. Difference of Microbial Community in the Stream Adjacent to the Mixed Antibiotic Effluent Source. TOXICS 2024; 12:135. [PMID: 38393230 PMCID: PMC10891948 DOI: 10.3390/toxics12020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/23/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024]
Abstract
Released antibiotics from source to stream can influence bacterial communities and potentially alter the ecosystem. This research provides a comprehensive examination of the sources, distribution, and bacterial community dynamics associated with varied antibiotic release sources adjacent to the stream. The residual of antibiotics from different sources was determined, and the bacterial community structure was examined to reveal the differences in the bacteria community in the stream. The residual of antibiotics was quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the Illumina MiSeq platform was utilized to sequence bacterial 16S rRNA genes, providing comprehensive insights into the bacterial community structure in the sediment across five different sites. Results indicated that the presence and distribution of antibiotics were significantly influenced by released sources. In the case of the bacterial community, the Proteobacteria and Firmicutes were the most dominant phyla in the sediment, and especially, the Firmicutes showed higher abundance in sites mostly affected by livestock sources. Additionally, livestock gut bacteria such as Clostridium saudiense, Proteiniclasticum ruminis, and Turicibacter sanguinis were prevalent in antibiotic-contaminated sites adjacent to livestock facilities. Overall, this study provides critical insights into the effect of antibiotic contamination by verifying the relationship between the occurrence of antibiotic residuals and the alteration in the bacterial community in the stream.
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Affiliation(s)
- Jin-Wook Kim
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Young-Kyu Hong
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Oh-Kyung Kwon
- Biogas Research Center, Hankyung National University, Anseong 17579, Republic of Korea
| | - Sung-Chul Kim
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
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16
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Ding FF, Li M, Wang T, Zhou NN, Qiao F, Du ZY, Zhang ML. Influence of dietary sodium taurocholate on the growth performance and liver health of Nile tilapia (Oreochromis niloticus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:319-330. [PMID: 36044098 DOI: 10.1007/s10695-022-01116-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Bile acids (BAs) are a class of cholesterol-derived amphipathic molecules approved as new animal feed additives. However, the functional researches mainly focused on BAs mixture, and the influence of the individual BA on fishes was still limited. In the present study, Nile tilapia were fed basal diet with three levels of sodium taurocholate at 0 mg/kg (CON), 300 mg/kg (TCAL), and 600 mg/kg (TCAH) for 8 weeks. The results indicated that addition of sodium taurocholate did not significantly influence the growth performance. Instead, TCAH group had higher cholesterol accumulation with liver fibrosis. In TCAH group, the level of nuclear factor E2-related factor 2 (nrf2) signaling-associated oxidative stress factors significantly increased in the liver. Additionally, fish in TCAH group had the highest expression level of genes encoding endoplasmic reticulum (ER) stress and inflammatory cytokines in the liver. In conclusion, 300 mg/kg of sodium taurocholate did not significantly influence the growth performance of fish, while 600 mg/kg of sodium taurocholate markedly induced cholesterol accumulation and liver injury, suggesting that the application of taurocholic acid in aquafeed should be re-evaluated.
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Affiliation(s)
- Fei-Fei Ding
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Miao Li
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Tong Wang
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Nan-Nan Zhou
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Qiao
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- LANEH, School of Life Sciences, East China Normal University, Shanghai, China.
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17
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Yin Q, Yu J, Li J, Zhang T, Wang T, Zhu Y, Zhang J, Yao J. Enhancing milk quality and modulating rectal microbiota of dairy goats in starch-rich diet: the role of bile acid supplementation. J Anim Sci Biotechnol 2024; 15:7. [PMID: 38247003 PMCID: PMC10801996 DOI: 10.1186/s40104-023-00957-7] [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: 07/13/2023] [Accepted: 10/29/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Diets rich in starch have been shown to increase a risk of reducing milk fat content in dairy goats. While bile acids (BAs) have been used as a lipid emulsifier in monogastric and aquatic animals, their effect on ruminants is not well understood. This study aimed to investigate the impact of BAs supplementation on various aspects of dairy goat physiology, including milk composition, rumen fermentation, gut microbiota, and BA metabolism. RESULTS We randomly divided eighteen healthy primiparity lactating dairy goats (days in milk = 100 ± 6 d) into two groups and supplemented them with 0 or 4 g/d of BAs undergoing 5 weeks of feeding on a starch-rich diet. The results showed that BAs supplementation positively influenced milk yield and improved the quality of fatty acids in goat milk. BAs supplementation led to a reduction in saturated fatty acids (C16:0) and an increase in monounsaturated fatty acids (cis-9 C18:1), resulting in a healthier milk fatty acid profile. We observed a significant increase in plasma total bile acid concentration while the proportion of rumen short-chain fatty acids was not affected. Furthermore, BAs supplementation induced significant changes in the composition of the gut microbiota, favoring the enrichment of specific bacterial groups and altering the balance of microbial populations. Correlation analysis revealed associations between specific bacterial groups (Bacillus and Christensenellaceae R-7 group) and BA types, suggesting a role for the gut microbiota in BA metabolism. Functional prediction analysis revealed notable changes in pathways associated with lipid metabolism, suggesting that BAs supplementation has the potential to modulate lipid-related processes. CONCLUSION These findings highlight the potential benefits of BAs supplementation in enhancing milk production, improving milk quality, and influencing metabolic pathways in dairy goats. Further research is warranted to elucidate the underlying mechanisms and explore the broader implications of these findings.
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Affiliation(s)
- Qingyan Yin
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
| | - Junjian Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
| | - Jiaxiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
| | - Tianci Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
| | - Tianyu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China
| | - Yufei Zhu
- DAYU Bioengineering (Xi'an) Industrial Development Research Institute, Xi'an, 710000, Shaanxi, P.R. China
| | - Jun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, Shaanxi, P.R. China.
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18
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Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J. Host genetic regulation of human gut microbial structural variation. Nature 2024; 625:813-821. [PMID: 38172637 PMCID: PMC10808065 DOI: 10.1038/s41586-023-06893-w] [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: 12/22/2022] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established1-6, little is known about how host genetics regulates the genetic diversity of gut microorganisms. Here we conducted a meta-analysis of associations between human genetic variation and gut microbial structural variation in 9,015 individuals from four Dutch cohorts. Strikingly, the presence rate of a structural variation segment in Faecalibacterium prausnitzii that harbours an N-acetylgalactosamine (GalNAc) utilization gene cluster is higher in individuals who secrete the type A oligosaccharide antigen terminating in GalNAc, a feature that is jointly determined by human ABO and FUT2 genotypes, and we could replicate this association in a Tanzanian cohort. In vitro experiments demonstrated that GalNAc can be used as the sole carbohydrate source for F. prausnitzii strains that carry the GalNAc-metabolizing pathway. Further in silico and in vitro studies demonstrated that other ABO-associated species can also utilize GalNAc, particularly Collinsella aerofaciens. The GalNAc utilization genes are also associated with the host's cardiometabolic health, particularly in individuals with mucosal A-antigen. Together, the findings of our study demonstrate that genetic associations across the human genome and bacterial metagenome can provide functional insights into the reciprocal host-microbiome relationship.
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Affiliation(s)
- Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Daoming Wang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Lei Liu
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Sergio Andreu-Sánchez
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Yue Zhang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Angel J Ruiz-Moreno
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Haoran Peng
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Niels Plomp
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Ángela Del Castillo-Izquierdo
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Ranko Gacesa
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Esteban A Lopera-Maya
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Godfrey S Temba
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vesla I Kullaya
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Sander S van Leeuwen
- University of Groningen, University Medical Center Groningen, Department of Laboratory Medicine, Groningen, The Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Serena Sanna
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- Institute for Genetic and Biomedical Research, National Research Council, Cagliari, Italy
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Hermie J M Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands.
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19
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Zhang C, Li G, Lu T, Liu L, Sui Y, Bai R, Li L, Sun B. The Interaction of Microbiome and Pancreas in Acute Pancreatitis. Biomolecules 2023; 14:59. [PMID: 38254659 PMCID: PMC10813032 DOI: 10.3390/biom14010059] [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: 11/29/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Acute pancreatitis (AP) is a common acute abdomen disease characterized by the pathological activation of digestive enzymes and the self-digestion of pancreatic acinar cells. Secondary infection and sepsis are independent prognosticators for AP progression and increased mortality. Accumulating anatomical and epidemiological evidence suggests that the dysbiosis of gut microbiota affects the etiology and severity of AP through intestinal barrier disruption, local or systemic inflammatory response, bacterial translocation, and the regulatory role of microbial metabolites in AP patients and animal models. Recent studies discussing the interactions between gut microbiota and the pancreas have opened new scopes for AP, and new therapeutic interventions that target the bacteria community have received substantial attention. This review concentrates on the alterations of gut microbiota and its roles in modulating gut-pancreas axis in AP. The potential therapies of targeting microbes as well as the major challenges of applying those interventions are explored. We expect to understand the roles of microbes in AP diagnosis and treatment.
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Affiliation(s)
- Can Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Guanqun Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Tianqi Lu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Liwei Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Yuhang Sui
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Rui Bai
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
| | - Le Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; (C.Z.)
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin 150001, China
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20
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Effenberger M, Grander C, Grabherr F, Tilg H. Nonalcoholic Fatty Liver Disease and the Intestinal Microbiome: An Inseparable Link. J Clin Transl Hepatol 2023; 11:1498-1507. [PMID: 38161503 PMCID: PMC10752805 DOI: 10.14218/jcth.2023.00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/21/2023] [Accepted: 07/18/2023] [Indexed: 01/03/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) particularly affects patients with type 2 diabetes and obesity. The incidence of NAFLD has increased significantly over the last decades and is now pandemically across the globe. It is a complex systemic disease comprising hepatic lipid accumulation, inflammation, lipotoxicity, gut dysbiosis, and insulin resistance as main features and with the potential to progress to cirrhosis and hepatocellular carcinoma (HCC). In numerous animal and human studies the gut microbiota plays a key role in the pathogenesis of NAFLD, NAFLD-cirrhosis and NAFLD-associated HCC. Lipotoxicity is the driver of inflammation, insulin resistance, and liver injury. Likewise, western diet, obesity, and metabolic disorders may alter the gut microbiota, which activates innate and adaptive immune responses and fuels hereby hepatic and systemic inflammation. Indigestible carbohydrates are fermented by the gut microbiota to produce important metabolites, such as short-chain fatty acids and succinate. Numerous animal and human studies suggested a pivotal role of these metabolites in the progression of NAFLD and its comorbidities. Though, modification of the gut microbiota and/or the metabolites could even be beneficial in patients with NAFLD, NAFLD-cirrhosis, and NAFLD-associated HCC. In this review we collect the evidence that exogenous and endogenous hits drive liver injury in NAFLD and propel liver fibrosis and the progressing to advanced disease stages. NAFLD can be seen as the product of a complex interplay between gut microbiota, the immune response and metabolism. Thus, the challenge will be to understand its pathogenesis and to develop new therapeutic strategies.
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Affiliation(s)
- Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Grander
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Felix Grabherr
- 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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21
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Ma C, Zhang Y, Jiang S, Teng F, Huang S, Zhang J. Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. mSystems 2023; 8:e0082823. [PMID: 37905808 PMCID: PMC10734426 DOI: 10.1128/msystems.00828-23] [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: 08/07/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.
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Affiliation(s)
- Chenchen Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yufeng Zhang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Fei Teng
- Qingdao Stomatological Hospital Affiliated to Qingdao University, Qingdao, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, Hainan, China
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22
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Liu R, Zou Y, Wang WQ, Chen JH, Zhang L, Feng J, Yin JY, Mao XY, Li Q, Luo ZY, Zhang W, Wang DM. Gut microbial structural variation associates with immune checkpoint inhibitor response. Nat Commun 2023; 14:7421. [PMID: 37973916 PMCID: PMC10654443 DOI: 10.1038/s41467-023-42997-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023] Open
Abstract
The gut microbiota may have an effect on the therapeutic resistance and toxicity of immune checkpoint inhibitors (ICIs). However, the associations between the highly variable genomes of gut bacteria and the effectiveness of ICIs remain unclear, despite the fact that merely a few gene mutations between similar bacterial strains may cause significant phenotypic variations. Here, using datasets from the gut microbiome of 996 patients from seven clinical trials, we systematically identify microbial genomic structural variants (SVs) using SGV-Finder. The associations between SVs and response, progression-free survival, overall survival, and immune-related adverse events are systematically explored by metagenome-wide association analysis and replicated in different cohorts. Associated SVs are located in multiple species, including Akkermansia muciniphila, Dorea formicigenerans, and Bacteroides caccae. We find genes that encode enzymes that participate in glucose metabolism be harbored in these associated regions. This work uncovers a nascent layer of gut microbiome heterogeneity that is correlated with hosts' prognosis following ICI treatment and represents an advance in our knowledge of the intricate relationships between microbiota and tumor immunotherapy.
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Affiliation(s)
- Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.
| | - You Zou
- Information and Network center, Central South University, Changsha, 410083, P.R. China
| | - Wei-Quan Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Jun-Hong Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Lei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Jia Feng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Xiao-Yuan Mao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Zhi-Ying Luo
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, PR China
- Institute of Clinical Pharmacy, Central South University, Changsha, PR China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China.
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.
| | - Dao-Ming Wang
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9713AV, the Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, 9713AV, the Netherlands.
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23
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Gou W, Miao Z, Deng K, Zheng JS. Nutri-microbiome epidemiology, an emerging field to disentangle the interplay between nutrition and microbiome for human health. Protein Cell 2023; 14:787-806. [PMID: 37099800 PMCID: PMC10636640 DOI: 10.1093/procel/pwad023] [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: 02/02/2023] [Accepted: 04/02/2023] [Indexed: 04/28/2023] Open
Abstract
Diet and nutrition have a substantial impact on the human microbiome, and interact with the microbiome, especially gut microbiome, to modulate various diseases and health status. Microbiome research has also guided the nutrition field to a more integrative direction, becoming an essential component of the rising area of precision nutrition. In this review, we provide a broad insight into the interplay among diet, nutrition, microbiome, and microbial metabolites for their roles in the human health. Among the microbiome epidemiological studies regarding the associations of diet and nutrition with microbiome and its derived metabolites, we summarize those most reliable findings and highlight evidence for the relationships between diet and disease-associated microbiome and its functional readout. Then, the latest advances of the microbiome-based precision nutrition research and multidisciplinary integration are described. Finally, we discuss several outstanding challenges and opportunities in the field of nutri-microbiome epidemiology.
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Affiliation(s)
- Wanglong Gou
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Zelei Miao
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Kui Deng
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Ju-Sheng Zheng
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
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24
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Yang P, Yang J, Long H, Huang K, Ji L, Lin H, Jiang X, Wang AK, Tian G, Ning K. MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality. IMETA 2023; 2:e131. [PMID: 38868224 PMCID: PMC10989818 DOI: 10.1002/imt2.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 06/14/2024]
Abstract
The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow. Data processing module: Uploaded data is processed to generate taxonomical distribution and functional composition results. Metagenome-wide association studies module (MWAS): Various methods, including biomarker analysis, PCA, co-occurrence networks, and sample classification, are employed using metadata. Data search module: Users can query nucleotide sequences to retrieve information in the MicroEXPERT database. Data visualization module: Visualization tools are used to illustrate the metagenome analysis results.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
- Institute of Medical GenomicsBiomedical Sciences College, Shandong First Medical UniversityJinanShandongChina
| | - Jialiang Yang
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
- Department of SciencesAcademician Workstation, Changsha Medical UniversityChangshaChina
| | - Haixia Long
- Department of Information Science TechnologyHainan Normal UniversityHaikouChina
| | - Kaimei Huang
- Department of MathematicsZhejiang Normal UniversityJinhuaChina
| | - Lei Ji
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Hanyang Lin
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | - Xiuli Jiang
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | | | - Geng Tian
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
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25
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Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon ATJ, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H. Gut microbial carbohydrate metabolism contributes to insulin resistance. Nature 2023; 621:389-395. [PMID: 37648852 PMCID: PMC10499599 DOI: 10.1038/s41586-023-06466-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
Insulin resistance is the primary pathophysiology underlying metabolic syndrome and type 2 diabetes1,2. Previous metagenomic studies have described the characteristics of gut microbiota and their roles in metabolizing major nutrients in insulin resistance3-9. In particular, carbohydrate metabolism of commensals has been proposed to contribute up to 10% of the host's overall energy extraction10, thereby playing a role in the pathogenesis of obesity and prediabetes3,4,6. Nevertheless, the underlying mechanism remains unclear. Here we investigate this relationship using a comprehensive multi-omics strategy in humans. We combine unbiased faecal metabolomics with metagenomics, host metabolomics and transcriptomics data to profile the involvement of the microbiome in insulin resistance. These data reveal that faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines. We identify gut bacteria associated with insulin resistance and insulin sensitivity that show a distinct pattern of carbohydrate metabolism, and demonstrate that insulin-sensitivity-associated bacteria ameliorate host phenotypes of insulin resistance in a mouse model. Our study, which provides a comprehensive view of the host-microorganism relationships in insulin resistance, reveals the impact of carbohydrate metabolism by microbiota, suggesting a potential therapeutic target for ameliorating insulin resistance.
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Affiliation(s)
- Tadashi Takeuchi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Tetsuya Kubota
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan.
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan.
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Division of Diabetes and Metabolism, The Institute for Medical Science Asahi Life Foundation, Tokyo, Japan.
- Department of Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Tokyo, Japan.
| | - Yumiko Nakanishi
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
| | - Hiroshi Tsugawa
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Andrew Tae-Jun Kwon
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Yoshiki Mochizuki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Toshimori Kitami
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Katsuyuki Yugi
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshiko Mizuno
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
- Development Bank of Japan, Tokyo, Japan
| | - Nobutake Yamamichi
- Center for Epidemiology and Preventive Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | | | - Iseki Takamoto
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Metabolism and Endocrinology, Tokyo Medical University Ibaraki Medical Center, Ami Town, Japan
| | - Naoto Kubota
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Toranomon Hospital, Tokyo, Japan
| | - Erik Arner
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Fondazione Human Technopole, Milan, Italy
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Shigeo Koyasu
- Laboratory for Immune Cell Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan.
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan.
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
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Du J, Wu W, Zhu B, Tao W, Liu L, Cheng X, Zhao M, Wu J, Li Y, Pei K. Recent advances in regulating lipid metabolism to prevent coronary heart disease. Chem Phys Lipids 2023; 255:105325. [PMID: 37414117 DOI: 10.1016/j.chemphyslip.2023.105325] [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: 05/11/2023] [Revised: 07/01/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
The pathogenesis of coronary heart disease is a highly complex process, with lipid metabolism disorders being closely linked to its development. Therefore, this paper analyzes the various factors that influence lipid metabolism, including obesity, genes, intestinal microflora, and ferroptosis, through a comprehensive review of basic and clinical studies. Additionally, this paper delves deeply into the pathways and patterns of coronary heart disease. Based on these findings, it proposes various intervention pathways and therapeutic methods, such as the regulation of lipoprotein enzymes, lipid metabolites, and lipoprotein regulatory factors, as well as the modulation of intestinal microflora and the inhibition of ferroptosis. Ultimately, this paper aims to offer new ideas for the prevention and treatment of coronary heart disease.
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Affiliation(s)
- Jingchun Du
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wei Wu
- Key laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Boran Zhu
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weiwei Tao
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lina Liu
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaolan Cheng
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Min Zhao
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jibiao Wu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Yunlun Li
- Innovation Research Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Ke Pei
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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Yan M, Pratama AA, Somasundaram S, Li Z, Jiang Y, Sullivan MB, Yu Z. Interrogating the viral dark matter of the rumen ecosystem with a global virome database. Nat Commun 2023; 14:5254. [PMID: 37644066 PMCID: PMC10465536 DOI: 10.1038/s41467-023-41075-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.
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Affiliation(s)
- Ming Yan
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Sripoorna Somasundaram
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Matthew B Sullivan
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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28
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Song Z, Feng S, Zhou X, Song Z, Li J, Li P. Taxonomic identification of bile salt hydrolase-encoding lactobacilli: Modulation of the enterohepatic bile acid profile. IMETA 2023; 2:e128. [PMID: 38867937 PMCID: PMC10989828 DOI: 10.1002/imt2.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 06/14/2024]
Abstract
Bile salt hydrolases (BSHs) are enzymes that are essential for the enterohepatic metabolism of bile acids (BAs). BSHs catalyze the production of unconjugated BAs and regulate the homeostasis of BA pool. This study identified Lactobacillus as a crucial BSH-encoding genus, and 16 main species were obtained using metagenomic data from publicly available human gut microbiome databases. Then, the 16 species of lactobacilli were classified into four typical categories by BSH phylotypes, including five species encoding BSH-T0, six species encoding BSH-T2, four species encoding BSH-T3, and Ligilactobacillus salivarius encoding both BSH-T0 and BSH-T3. The lactobacilli with the highest in vitro deconjugation activities against seven conjugated BAs were the BSH-T3-encoding strains. Furthermore, in vivo studies in mice administered four representative lactobacilli strains encoding different BSH phylotypes showed that treatment with BSH-T3-encoding Limosilactobacillus reuteri altered the structure of the gut microbiome and metabolome and significantly increased the levels of unconjugated BAs and total BA excretion. Our findings facilitated the taxonomic identification of crucial BSH-encoding lactobacilli in human gut microbiota and shed light on their contributions toward modulation of the enterohepatic circulation of BAs, which will contribute to future therapeutic applications of BSH-encoding probiotics to improve human health.
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Affiliation(s)
- Ziwei Song
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjingChina
| | - Shuo Feng
- School of Life Science and TechnologyChina Pharmaceutical UniversityNanjingChina
| | - Xingchen Zhou
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Disease, Department of BiotechnologyBeijing Institute of Radiation MedicineBeijingChina
| | - Zhengxing Song
- School of Life Science and TechnologyChina Pharmaceutical UniversityNanjingChina
| | - Jing Li
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjingChina
- School of Life Science and TechnologyChina Pharmaceutical UniversityNanjingChina
| | - Ping Li
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjingChina
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29
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Cai Y, Liu P, Zhou X, Yuan J, Chen Q. Probiotics therapy show significant improvement in obesity and neurobehavioral disorders symptoms. Front Cell Infect Microbiol 2023; 13:1178399. [PMID: 37249983 PMCID: PMC10213414 DOI: 10.3389/fcimb.2023.1178399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Obesity is a complex metabolic disease, with cognitive impairment being an essential complication. Gut microbiota differs markedly between individuals with and without obesity. The microbial-gut-brain axis is an important pathway through which metabolic factors, such as obesity, affect the brain. Probiotics have been shown to alleviate symptoms associated with obesity and neurobehavioral disorders. In this review, we evaluated previously published studies on the effectiveness of probiotic interventions in reducing cognitive impairment, depression, and anxiety associated with obesity or a high-fat diet. Most of the probiotics studied have beneficial health effects on obesity-induced cognitive impairment and anxiety. They positively affect immune regulation, the hypothalamic-pituitary-adrenal axis, hippocampal function, intestinal mucosa protection, and glucolipid metabolism regulation. Probiotics can influence changes in the composition of the gut microbiota and the ratio between various flora. However, probiotics should be used with caution, particularly in healthy individuals. Future research should further explore the mechanisms underlying the gut-brain axis, obesity, and cognitive function while overcoming the significant variation in study design and high risk of bias in the current evidence.
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30
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Wang S, Xu C, Liu H, Wei W, Zhou X, Qian H, Zhou L, Zhang H, Wu L, Zhu C, Yang Y, He L, Li K. Connecting the Gut Microbiota and Neurodegenerative Diseases: the Role of Bile Acids. Mol Neurobiol 2023:10.1007/s12035-023-03340-9. [PMID: 37121952 DOI: 10.1007/s12035-023-03340-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/04/2023] [Indexed: 05/02/2023]
Abstract
With the acceleration of global population aging, neurodegenerative diseases (NDs) will become the second leading cause of death in the world, which seriously threatens human life and health. Alzheimer's disease and Parkinson's disease are the most common and typical NDs. The exact mechanisms of the NDs occurrence and development remain unclear, which may be related to immune, oxidative stress, and abnormal aggregation of pathogenic proteins. Studies have suggested that gut microbiota (GM) influences brain function and plays an important role in regulating emotional and cognitive function. Recently, bile acids (BAs) have become the "star molecule" in the microbiota-gut-brain (MGB) axis research. BAs have been reported to exert anti-inflammatory, antioxidant, and neuroprotective activities in NDs. However, the role of BAs in the connection between GM and the central nervous system (CNS) is still unclear. In this review, we will review the possible mechanisms of BAs between GM and NDs and explore the function of BAs to provide ideas for the prevention and treatment of NDs in the future.
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Affiliation(s)
- Shixu Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
| | - Chongchong Xu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
| | - Hongyan Liu
- The Mental Hospital of Yunnan Province, Mental Health Center affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Wei Wei
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
| | - Xuemei Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
| | - Haipeng Qian
- Department of Nursing, AnHui College of Traditional Chinese Medicine, Wuhu, Anhui Province, China
| | - Li Zhou
- The Mental Hospital of Yunnan Province, Mental Health Center affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Haiqing Zhang
- The Mental Hospital of Yunnan Province, Mental Health Center affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Li Wu
- The Mental Hospital of Yunnan Province, Mental Health Center affiliated to Kunming Medical University, Kunming, Yunnan Province, China
| | - Chen Zhu
- Department of Physical Education, Kunming Medical University, Kunming, Yunnan Province, China
| | - Yuting Yang
- Computer Science and Technology of Department of Science and Engineering, Shiyuan College of Nanninng Normal University, Nanning, Guangxi Province, China
| | - Lin He
- The Mental Hospital of Yunnan Province, Mental Health Center affiliated to Kunming Medical University, Kunming, Yunnan Province, China.
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China.
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong Province, China.
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31
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Fan Y, Ying J, Ma H, Cui H. Microbiota-related metabolites fueling the understanding of ischemic heart disease. IMETA 2023; 2:e94. [PMID: 38868424 PMCID: PMC10989774 DOI: 10.1002/imt2.94] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/04/2023] [Accepted: 01/21/2023] [Indexed: 06/14/2024]
Abstract
Up-to-date knowledge of gut microbial taxa associated with ischemic heart disease (IHD). Microbial metabolites for mechanistic dissection of IHD pathology. Microbiome-based therapies in IHD prevention and treatment.
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Affiliation(s)
- Yong Fan
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Jiajun Ying
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
- Department of Cardiology, Ningbo First HospitalNingbo UniversityNingboChina
| | - Hongchuang Ma
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
| | - Hanbin Cui
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang ProvinceNingboChina
- Department of Cardiology, Ningbo First HospitalNingbo UniversityNingboChina
- Ningbo Clinical Research Center for Cardiovascular DiseaseNingboChina
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32
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Fan Y, Støving RK, Berreira Ibraim S, Hyötyläinen T, Thirion F, Arora T, Lyu L, Stankevic E, Hansen TH, Déchelotte P, Sinioja T, Ragnarsdottir O, Pons N, Galleron N, Quinquis B, Levenez F, Roume H, Falony G, Vieira-Silva S, Raes J, Clausen L, Telléus GK, Bäckhed F, Oresic M, Ehrlich SD, Pedersen O. The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Nat Microbiol 2023; 8:787-802. [PMID: 37069399 PMCID: PMC10159860 DOI: 10.1038/s41564-023-01355-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023]
Abstract
Anorexia nervosa (AN) is an eating disorder with a high mortality. About 95% of cases are women and it has a population prevalence of about 1%, but evidence-based treatment is lacking. The pathogenesis of AN probably involves genetics and various environmental factors, and an altered gut microbiota has been observed in individuals with AN using amplicon sequencing and relatively small cohorts. Here we investigated whether a disrupted gut microbiota contributes to AN pathogenesis. Shotgun metagenomics and metabolomics were performed on faecal and serum samples, respectively, from a cohort of 77 females with AN and 70 healthy females. Multiple bacterial taxa (for example, Clostridium species) were altered in AN and correlated with estimates of eating behaviour and mental health. The gut virome was also altered in AN including a reduction in viral-bacterial interactions. Bacterial functional modules associated with the degradation of neurotransmitters were enriched in AN and various structural variants in bacteria were linked to metabolic features of AN. Serum metabolomics revealed an increase in metabolites associated with reduced food intake (for example, indole-3-propionic acid). Causal inference analyses implied that serum bacterial metabolites are potentially mediating the impact of an altered gut microbiota on AN behaviour. Further, we performed faecal microbiota transplantation from AN cases to germ-free mice under energy-restricted feeding to mirror AN eating behaviour. We found that the reduced weight gain and induced hypothalamic and adipose tissue gene expression were related to aberrant energy metabolism and eating behaviour. Our 'omics' and mechanistic studies imply that a disruptive gut microbiome may contribute to AN pathogenesis.
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Affiliation(s)
- Yong Fan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - René Klinkby Støving
- Center for Eating Disorders, Odense University Hospital, and Research Unit for Medical Endocrinology, Mental Health Services in the Region of Southern Denmark, Open Patient data Explorative Network (OPEN) and Clinical Institute, University of Southern Denmark, Odense, Denmark
| | | | | | | | - Tulika Arora
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Liwei Lyu
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, University of Copenhagen and Herlev-Gentofte University Hospital, Copenhagen, Denmark
| | - Evelina Stankevic
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Pierre Déchelotte
- INSERM U1073 Research Unit and TargEDys, Rouen University, Rouen, France
| | - Tim Sinioja
- School of Science and Technology, Örebro University, Örebro, Sweden
| | | | - Nicolas Pons
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | | | | | | | - Hugo Roume
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Gwen Falony
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sara Vieira-Silva
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jeroen Raes
- Laboratory of Molecular bacteriology, Department of Microbiology and Immunology, Rega Institute Ku Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Loa Clausen
- Department of Child and Adolescent Psychiatry, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Gry Kjaersdam Telléus
- Unit for Psychiatric Research, Aalborg University Hospital, Aalborg, Denmark
- Department of Communication and Psychology, The Faculty of Social Sciences and Humanities, Aalborg University, Aalborg, Denmark
| | - Fredrik Bäckhed
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Matej Oresic
- School of Medical Sciences, Örebro University, Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - S Dusko Ehrlich
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
- Department of Clinical and Movement Neurosciences, University College London, London, UK
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.
- Department of Medicine, University of Copenhagen and Herlev-Gentofte University Hospital, Copenhagen, Denmark.
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33
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Palasantzas VEJM, Tamargo-Rubio I, Le K, Slager J, Wijmenga C, Jonkers IH, Kumar V, Fu J, Withoff S. iPSC-derived organ-on-a-chip models for personalized human genetics and pharmacogenomics studies. Trends Genet 2023; 39:268-284. [PMID: 36746737 DOI: 10.1016/j.tig.2023.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/24/2022] [Accepted: 01/12/2023] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) have now correlated hundreds of genetic variants with complex genetic diseases and drug efficacy. Functional characterization of these factors remains challenging, particularly because of the lack of human model systems. Molecular and nanotechnological advances, in particular the ability to generate patient-specific PSC lines, differentiate them into diverse cell types, and seed and combine them on microfluidic chips, have led to the establishment of organ-on-a-chip (OoC) platforms that recapitulate organ biology. OoC technology thus provides unique personalized platforms for studying the effects of host genetics and environmental factors on organ physiology. In this review we describe the technology and provide examples of how OoCs may be used for disease modeling and pharmacogenetic research.
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Affiliation(s)
- Victoria E J M Palasantzas
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Isabel Tamargo-Rubio
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kieu Le
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jelle Slager
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Internal Medicine and Radboud Centre for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Gillard J, Leclercq IA. Biological tuners to reshape the bile acid pool for therapeutic purposes in non-alcoholic fatty liver disease. Clin Sci (Lond) 2023; 137:65-85. [PMID: 36601783 PMCID: PMC9816373 DOI: 10.1042/cs20220697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023]
Abstract
Bile acids synthesized within the hepatocytes are transformed by gut microorganisms and reabsorbed into the portal circulation. During their enterohepatic cycling, bile acids act as signaling molecules by interacting with receptors to regulate pathways involved in many physiological processes. The bile acid pool, composed of a variety of bile acid species, has been shown to be altered in diseases, hence contributing to disease pathogenesis. Thus, understanding the changes in bile acid pool size and composition in pathological processes will help to elaborate effective pharmacological treatments. Five crucial steps along the enterohepatic cycle shape the bile acid pool size and composition, offering five possible targets for therapeutic intervention. In this review, we provide an insight on the strategies to modulate the bile acid pool, and then we discuss the potential benefits in non-alcoholic fatty liver disease.
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Affiliation(s)
- Justine Gillard
- Laboratory of Hepato‐Gastroenterology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Isabelle A. Leclercq
- Laboratory of Hepato‐Gastroenterology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
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35
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Lin L, Lai Z, Yang H, Zhang J, Qi W, Xie F, Mao S. Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. THE ISME JOURNAL 2023; 17:172-184. [PMID: 36261508 PMCID: PMC9750977 DOI: 10.1038/s41396-022-01333-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.
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Affiliation(s)
- Limei Lin
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zheng Lai
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Huisheng Yang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiyou Zhang
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weibiao Qi
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fei Xie
- grid.27871.3b0000 0000 9750 7019Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China ,grid.27871.3b0000 0000 9750 7019Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China. .,Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Huang Y, Lu W, Zeng M, Hu X, Su Z, Liu Y, Liu Z, Yuan J, Li L, Zhang X, Huang L, Hu W, Wang X, Li S, Zhang H. Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health. MICROBIOME 2022; 10:245. [PMID: 36581858 PMCID: PMC9801562 DOI: 10.1186/s40168-022-01437-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/25/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD. METHODS Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis. RESULTS Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD. CONCLUSIONS We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.
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Affiliation(s)
- Yuan Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Wenlong Lu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Min Zeng
- PICU, Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaoyue Hu
- Department of Neonatology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Zhanhao Su
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Yiwei Liu
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zeye Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Jianhui Yuan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Li Li
- Department of Neonatology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Xiaoling Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China
| | - Long Huang
- Shanghai Majorbio Bio-Pharm Technology Co, Shanghai, China
| | - Wanjin Hu
- Shanghai Majorbio Bio-Pharm Technology Co, Shanghai, China
| | - Xu Wang
- PICU, Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shoujun Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China.
| | - Hao Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Pediatric Cardiac Surgery Center, Fuwai Hospital, Chinese Academy of Medical Sciences, and Peking Union Medical College, Beijing, China.
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Research Progress on the Therapeutic Effect of Polysaccharides on Non-Alcoholic Fatty Liver Disease through the Regulation of the Gut–Liver Axis. Int J Mol Sci 2022; 23:ijms231911710. [PMID: 36233011 PMCID: PMC9570256 DOI: 10.3390/ijms231911710] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease affecting global public health at present, which can induce cirrhosis and liver cancer in serious cases. However, NAFLD is a multifactorial disease, and there is still a lack of research on its mechanism and therapeutic strategy. With the development of the gut–liver axis theory, the association between the gut–liver axis and the pathogenesis of NAFLD has been gradually disclosed. Polysaccharides, as a kind of natural product, have the advantages of low toxicity, multi-target and multi-pathway action. It has been reported that polysaccharides can affect the gut–liver axis at multiple interrelated levels, such as maintaining the ecological balance of gut microbiota (GM), regulating the metabolites of GM and improving the intestinal barrier function, which thereby plays a protective role in NAFLD. These studies have great scientific significance in understanding NAFLD based on the gut–liver axis and developing safe and effective medical treatments. Herein, we reviewed the recent progress of polysaccharides in improving nonalcoholic fatty liver disease (NAFLD) through the gut–liver axis.
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38
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West PT, Chanin RB, Bhatt AS. From genome structure to function: insights into structural variation in microbiology. Curr Opin Microbiol 2022; 69:102192. [PMID: 36030622 PMCID: PMC9783807 DOI: 10.1016/j.mib.2022.102192] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 12/27/2022]
Abstract
Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomes and metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.
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Affiliation(s)
- Patrick T West
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Rachael B Chanin
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA.
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39
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Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:ijms23179834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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40
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Li Y, Zhao P, Zhang Y, Zhen J, Zhao L, Cai Y, Lu Q, Huang G. Fecal-associated microbiome differences between phlegm-dampness constitution and balanced constitution. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2022. [DOI: 10.1016/j.jtcms.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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41
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Short- and long-read metagenomics expand individualized structural variations in gut microbiomes. Nat Commun 2022; 13:3175. [PMID: 35676264 PMCID: PMC9177567 DOI: 10.1038/s41467-022-30857-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023] Open
Abstract
In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome. Here, Wang and colleagues combine short and long sequencing reads to characterize structural variations, prophage and CRISPR spacer elements in human gut microbiomes, and reveal functional differences at a finer level of bacterial strains.
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42
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Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes. Mucosal Immunol 2022; 15:1071-1084. [PMID: 35970917 DOI: 10.1038/s41385-022-00553-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023]
Abstract
Advances in technology and software have radically expanded the scope of metabolomics studies and allow us to monitor a broad transect of central carbon metabolism in routine studies. These increasingly sophisticated tools have shown that many human diseases are modulated by microbial metabolism. Despite this, it remains surprisingly difficult to move beyond these statistical associations and identify the specific molecular mechanisms that link dysbiosis to the progression of human disease. This difficulty stems from both the biological intricacies of host-microbiome dynamics as well as the analytical complexities inherent to microbiome metabolism research. The primary objective of this review is to examine the experimental and computational tools that can provide insights into the molecular mechanisms at work in host-microbiome interactions and to highlight the undeveloped frontiers that are currently holding back microbiome research from fully leveraging the benefits of modern metabolomics.
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Wang Y, Dong Q, Hu S, Zou H, Wu T, Shi J, Zhang H, Sheng Y, Sun W, Kong X, Chen L. Decoding microbial genomes to understand their functional roles in human complex diseases. IMETA 2022; 1:e14. [PMID: 38868571 PMCID: PMC10989872 DOI: 10.1002/imt2.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/20/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2024]
Abstract
Complex diseases such as cardiovascular disease (CVD), obesity, inflammatory bowel disease (IBD), kidney disease, type 2 diabetes (T2D), and cancer have become a major burden to public health and affect more than 20% of the population worldwide. The etiology of complex diseases is not yet clear, but they are traditionally thought to be caused by genetics and environmental factors (e.g., dietary habits), and by their interactions. Besides this, increasing pieces of evidence now highlight that the intestinal microbiota may contribute substantially to the health and disease of the human host via their metabolic molecules. Therefore, decoding the microbial genomes has been an important strategy to shed light on their functional potential. In this review, we summarize the roles of the gut microbiome in complex diseases from its functional perspective. We further introduce artificial tools in decoding microbial genomes to profile their functionalities. Finally, state-of-the-art techniques have been highlighted which may contribute to a mechanistic understanding of the gut microbiome in human complex diseases and promote the development of the gut microbiome-based personalized medicine.
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Affiliation(s)
- Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat‐Sen UniversitySun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
| | - Haifeng Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Yanhui Sheng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsuChina
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu SchoolNanjing Medical UniversitySuzhouJiangsuChina
- Department of Genetics, University Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
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44
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Affiliation(s)
- Alessia Perino
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristina Schoonjans
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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45
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Gut microbiota and its role in stress-induced hyperalgesia: gender-specific responses linked to different changes in serum metabolites. Pharmacol Res 2022; 177:106129. [DOI: 10.1016/j.phrs.2022.106129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022]
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46
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Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022; 38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.
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Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Rinse K Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome. Nat Med 2022; 28:2333-2343. [PMID: 36216932 PMCID: PMC9671809 DOI: 10.1038/s41591-022-02014-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/15/2022] [Indexed: 01/14/2023]
Abstract
The levels of the thousands of metabolites in the human plasma metabolome are strongly influenced by an individual's genetics and the composition of their diet and gut microbiome. Here, by assessing 1,183 plasma metabolites in 1,368 extensively phenotyped individuals from the Lifelines DEEP and Genome of the Netherlands cohorts, we quantified the proportion of inter-individual variation in the plasma metabolome explained by different factors, characterizing 610, 85 and 38 metabolites as dominantly associated with diet, the gut microbiome and genetics, respectively. Moreover, a diet quality score derived from metabolite levels was significantly associated with diet quality, as assessed by a detailed food frequency questionnaire. Through Mendelian randomization and mediation analyses, we revealed putative causal relationships between diet, the gut microbiome and metabolites. For example, Mendelian randomization analyses support a potential causal effect of Eubacterium rectale in decreasing plasma levels of hydrogen sulfite-a toxin that affects cardiovascular function. Lastly, based on analysis of the plasma metabolome of 311 individuals at two time points separated by 4 years, we observed a positive correlation between the stability of metabolite levels and the amount of variance in the levels of that metabolite that could be explained in our analysis. Altogether, characterization of factors that explain inter-individual variation in the plasma metabolome can help design approaches for modulating diet or the gut microbiome to shape a healthy metabolome.
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