151
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Bile acid metabolites control T H17 and T reg cell differentiation. Nature 2019; 576:143-148. [PMID: 31776512 PMCID: PMC6949019 DOI: 10.1038/s41586-019-1785-z] [Citation(s) in RCA: 692] [Impact Index Per Article: 138.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/17/2019] [Indexed: 02/06/2023]
Abstract
Bile acids are abundant in the mammalian gut, where they undergo bacteria-mediated transformation to generate a large pool of bioactive molecules. Although bile acids are known to affect host metabolism, cancer progression and innate immunity, it is unknown whether they affect adaptive immune cells such as T helper cells that express IL-17a (TH17 cells) or regulatory T cells (Treg cells). Here we screen a library of bile acid metabolites and identify two distinct derivatives of lithocholic acid (LCA), 3-oxoLCA and isoalloLCA, as T cell regulators in mice. 3-OxoLCA inhibited the differentiation of TH17 cells by directly binding to the key transcription factor retinoid-related orphan receptor-γt (RORγt) and isoalloLCA increased the differentiation of Treg cells through the production of mitochondrial reactive oxygen species (mitoROS), which led to increased expression of FOXP3. The isoalloLCA-mediated enhancement of Treg cell differentiation required an intronic Foxp3 enhancer, the conserved noncoding sequence (CNS) 3; this represents a mode of action distinct from that of previously identified metabolites that increase Treg cell differentiation, which require CNS1. The administration of 3-oxoLCA and isoalloLCA to mice reduced TH17 cell differentiation and increased Treg cell differentiation, respectively, in the intestinal lamina propria. Our data suggest mechanisms through which bile acid metabolites control host immune responses, by directly modulating the balance of TH17 and Treg cells.
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152
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Tanaka M, Sanefuji M, Morokuma S, Yoden M, Momoda R, Sonomoto K, Ogawa M, Kato K, Nakayama J. The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants. Gut Microbes 2019; 11:205-216. [PMID: 31550982 PMCID: PMC7053967 DOI: 10.1080/19490976.2019.1650997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The gut microbial community greatly changes in early life, influencing infant health and subsequent host physiology, notably through its collective metabolism, including host-microbiota interplay of bile acid (BA) metabolism. However, little is known regarding how the development of the intestinal microbial community is associated with maturation of intestinal BA metabolism. To address this, we monitored the succession of gut bacterial community and its association with fecal BA profile in the first 3 y of ten healthy Japanese infants. The BA profiles were classified into four types, defined by high content of conjugated primary BA (Con type), unconjugated primary BA (chenodeoxycholic acid and cholic acid) (Pri type), ursodeoxycholic acid (Urs type), and deoxycholic and lithocholic acid (Sec type). Most subjects begun with Con type or Pri type profiles during lactation and eventually transited to Sec type through Urs type after the start of solid food intake. Con type and Pri type were associated with Enterobacteriaceae-dominant microbiota corresponding to the neonatal type or Bifidobacterium-dominant microbiota corresponding to lactation type, respectively. Urs type subjects were strongly associated with Ruminococcus gnavus colonization, mostly occurring between Pri type and Sec type. Sec type was associated with adult-type complex microbiota dominated by a variety of Firmicutes and Bacteroidetes species. Addressing the link of the common developmental passage of intestinal BA metabolism with infant's health and subsequent host physiology requires further study.
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Affiliation(s)
- Masaru Tanaka
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Masafumi Sanefuji
- Research Center for Environment and Developmental Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Seiichi Morokuma
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Misako Yoden
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Rie Momoda
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Masanobu Ogawa
- Research Center for Environment and Developmental Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan,CONTACT Jiro Nakayama Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
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153
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Miller WB, Torday JS, Baluška F. The N-space Episenome unifies cellular information space-time within cognition-based evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:112-139. [PMID: 31415772 DOI: 10.1016/j.pbiomolbio.2019.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.
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Affiliation(s)
| | - John S Torday
- Department of Pediatrics, Harbor-UCLA Medical Center, USA.
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154
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Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A. Nutrient Sensing in CD11c Cells Alters the Gut Microbiota to Regulate Food Intake and Body Mass. Cell Metab 2019; 30:364-373.e7. [PMID: 31130466 PMCID: PMC6687538 DOI: 10.1016/j.cmet.2019.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/08/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial dysbiosis and inflammation are implicated in diet-induced obesity and insulin resistance. However, it is not known whether crosstalk between immunity and microbiota also regulates metabolic homeostasis in healthy animals. Here, we report that genetic deletion of tuberous sclerosis 1 (Tsc1) in CD11c+ myeloid cells (Tsc1f/fCD11cCre mice) reduced food intake and body mass in the absence of metabolic disease. Co-housing and fecal transplant experiments revealed a dominant role for the healthy gut microbiota in regulation of body weight. 16S rRNA sequencing, selective culture, and reconstitution experiments further confirmed that selective deficiency of Lactobacillus johnsonii Q1-7 contributed to decreased food intake and body mass in Tsc1f/fCD11cCre mice. Mechanistically, activation of mTORC1 signaling in CD11c cells regulated production of L. johnsonii Q1-7-specific IgA, allowing for its stable colonization in the gut. Together, our findings reveal an unexpected transkingdom immune-microbiota feedback loop for homeostatic regulation of food intake and body mass in mammals.
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Affiliation(s)
- D Nyasha Chagwedera
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA
| | - Qi Yan Ang
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Yew Ann Leong
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA; Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Kirthana Ganeshan
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA
| | - Jingwei Cai
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Ajay Chawla
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143-0795, USA; Departments of Physiology and Medicine, University of California, San Francisco, San Francisco, CA 94143-0795, USA.
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155
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Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease. Mediators Inflamm 2019; 2019:7659509. [PMID: 31341422 PMCID: PMC6613006 DOI: 10.1155/2019/7659509] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 02/08/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a major health threat around the world and is characterized by dysbiosis. Primary bile acids are synthesized in the liver and converted into secondary bile acids by gut microbiota. Recent studies support the role of bile acids in modulating dysbiosis and NAFLD, while the mechanisms are not well elucidated. Dysbiosis may alter the size and the composition of the bile acid pool, resulting in reduced signaling of bile acid receptors such as farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5). These receptors are essential in lipid and glucose metabolism, and impaired bile acid signaling may cause NAFLD. Bile acids also reciprocally regulate the gut microbiota directly via antibacterial activity and indirectly via FXR. Therefore, bile acid signaling is closely linked to dysbiosis and NAFLD. During the past decade, stimulation of bile acid receptors with their agonists has been extensively explored for the treatment of NAFLD in both animal models and clinical trials. Early evidence has suggested the potential of bile acid receptor agonists in NAFLD management, but their long-term safety and effectiveness need further clarification.
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156
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Descamps HC, Herrmann B, Wiredu D, Thaiss CA. The path toward using microbial metabolites as therapies. EBioMedicine 2019; 44:747-754. [PMID: 31201140 PMCID: PMC6606739 DOI: 10.1016/j.ebiom.2019.05.063] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/26/2022] Open
Abstract
Metabolites have emerged as the quintessential effectors mediating the impact of the commensal microbiome on human physiology, both locally at the sites of microbial colonization and systemically. The endocrine activity of the microbiome and its involvement in a multitude of complex diseases has made microbiome-modulated metabolites an attractive target for the development of new therapies. Several properties make metabolites uniquely suited for interventional strategies: natural occurrence in a broad range of concentrations, functional pleiotropy, ease of administration, and tissue bioavailability. Here, we provide an overview of recently discovered physiological effects of microbiome-associated small molecules that may serve as the first examples of metabolite-based therapies. We also highlight challenges and obstacles that the field needs to overcome on the path toward successful clinical trials of microbial metabolites for human disease.
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Affiliation(s)
- Hélène C Descamps
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Herrmann
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daphne Wiredu
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christoph A Thaiss
- Microbiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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157
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Parasar B, Zhou H, Xiao X, Shi Q, Brito IL, Chang PV. Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity. ACS CENTRAL SCIENCE 2019; 5:867-873. [PMID: 31139722 PMCID: PMC6535767 DOI: 10.1021/acscentsci.9b00147] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 05/26/2023]
Abstract
The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.
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Affiliation(s)
- Bibudha Parasar
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Hao Zhou
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Xieyue Xiao
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Qiaojuan Shi
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Ilana L. Brito
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Pamela V. Chang
- Department
of Chemistry and Chemical Biology, Department of Microbiology, Meinig School of Biomedical
Engineering, Center for Infection and Pathobiology, Cornell Institute of Host-Microbe
Interactions & Disease, and Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, United States
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158
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Pathogen Colonization Resistance in the Gut and Its Manipulation for Improved Health. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1300-1310. [PMID: 31100210 DOI: 10.1016/j.ajpath.2019.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/15/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Mammals have coevolved with a large community of symbiotic, commensal, and some potentially pathogenic microbes. The trillions of bacteria and hundreds of species in our guts form a relatively stable community that resists invasion by outsiders, including pathogens. This powerful protective force is referred to as colonization resistance. We discuss the variety of proposed or demonstrated mechanisms that can mediate colonization resistance and some potential ways to manipulate them for improved human health. Instances in which certain bacterial pathogens can overcome colonization resistance are also discussed.
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159
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Abstract
Bile acids facilitate nutrient absorption and are endogenous ligands for nuclear receptors that regulate lipid and energy metabolism. The brain-gut-liver axis plays an essential role in maintaining overall glucose, bile acid, and immune homeostasis. Fasting and feeding transitions alter nutrient content in the gut, which influences bile acid composition and pool size. In turn, bile acid signaling controls lipid and glucose use and protection against inflammation. Altered bile acid metabolism resulting from gene mutations, high-fat diets, alcohol, or circadian disruption can contribute to cholestatic and inflammatory diseases, diabetes, and obesity. Bile acids and their derivatives are valuable therapeutic agents for treating these inflammatory metabolic diseases.
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Affiliation(s)
- John Y L Chiang
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272;
| | - Jessica M Ferrell
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272;
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160
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Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract. PLoS Pathog 2019; 15:e1007581. [PMID: 30845232 PMCID: PMC6405046 DOI: 10.1371/journal.ppat.1007581] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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161
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Ding Y, Yanagi K, Cheng C, Alaniz RC, Lee K, Jayaraman A. Interactions between gut microbiota and non-alcoholic liver disease: The role of microbiota-derived metabolites. Pharmacol Res 2019; 141:521-529. [PMID: 30660825 PMCID: PMC6392453 DOI: 10.1016/j.phrs.2019.01.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023]
Abstract
There is increasing evidence that the intestinal microbiota plays a mechanistic role in the etiology of non-alcoholic fatty liver disease (NAFLD). Animal and human studies have linked small molecule metabolites produced by commensal bacteria in the gut contribute to not only intestinal inflammation, but also to hepatic inflammation. These immunomodulatory metabolites are capable of engaging host cellular receptors, and may mediate the observed association between gut dysbiosis and NAFLD. This review focuses on the effects and potential mechanisms of three specific classes of metabolites that synthesized or modified by gut bacteria: short chain fatty acids, amino acid catabolites, and bile acids. In particular, we discuss their role as ligands for cell surface and nuclear receptors regulating metabolic and inflammatory pathways in the intestine and liver. Studies reveal that the metabolites can both agonize and antagonize their cognate receptors to reduce or exacerbate liver steatosis and inflammation, and that the effects are metabolite- and context-specific. Further studies are warranted to more comprehensively understand bacterial metabolite-mediated gut-liver in NAFLD. This understanding could help identify novel therapeutics and therapeutic targets to intervene in the disease through the gut microbiota.
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Affiliation(s)
- Yufang Ding
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Karin Yanagi
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Clint Cheng
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA.
| | - Arul Jayaraman
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, 77807, USA; Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843, USA.
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162
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Song Z, Cai Y, Lao X, Wang X, Lin X, Cui Y, Kalavagunta PK, Liao J, Jin L, Shang J, Li J. Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. MICROBIOME 2019; 7:9. [PMID: 30674356 PMCID: PMC6345003 DOI: 10.1186/s40168-019-0628-3] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the composition of bile acids are found in many diseases caused by dysbacteriosis. RESULTS Here, we present the taxonomic identification of bile salt hydrolase (BSH) in human microbiota and elucidate the abundance and activity differences of various bacterial BSH among 11 different populations from six continents. For the first time, we revealed that bile salt hydrolase protein sequences (BSHs) are distributed in 591 intestinal bacterial strains within 117 genera in human microbiota, and 27.52% of these bacterial strains containing BSH paralogs. Significant variations are observed in BSH distribution patterns among different populations. Based on phylogenetic analysis, we reclassified these BSHs into eight phylotypes and investigated the abundance patterns of these phylotypes among different populations. From the inspection of enzyme activity among different BSH phylotypes, BSH-T3 showed the highest enzyme activity and is only found in Lactobaclillus. The phylotypes of BSH-T5 and BSH-T6 mainly from Bacteroides with high percentage of paralogs exhibit different enzyme activity and deconjugation activity. Furthermore, we found that there were significant differences between healthy individuals and patients with atherosclerosis and diabetes in some phylotypes of BSHs though the correlations were pleiotropic. CONCLUSION This study revealed the taxonomic and abundance profiling of BSH in human gut microbiome and provided a phylogenetic-based system to assess BSHs activity by classifying the target sequence into specific phylotype. Furthermore, the present work disclosed the variation patterns of BSHs among different populations of geographical regions and health/disease cohorts, which is essential to understand the role of BSH in the development and progression of related diseases.
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Affiliation(s)
- Ziwei Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Yuanyuan Cai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Xingzhen Lao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Xue Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Xiaoxuan Lin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Yingyun Cui
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | | | - Jun Liao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Liang Jin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Jing Shang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Jing Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
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163
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Alimov I, Menon S, Cochran N, Maher R, Wang Q, Alford J, Concannon JB, Yang Z, Harrington E, Llamas L, Lindeman A, Hoffman G, Schuhmann T, Russ C, Reece-Hoyes J, Canham SM, Cai X. Bile acid analogues are activators of pyrin inflammasome. J Biol Chem 2019; 294:3359-3366. [PMID: 30647128 DOI: 10.1074/jbc.ra118.005103] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
Bile acids are critical metabolites in the gastrointestinal tract and contribute to maintaining intestinal immune homeostasis through cross-talk with the gut microbiota. The conversion of bile acids by the gut microbiome is now recognized as a factor affecting both host metabolism and immune responses, but its physiological roles remain unclear. We conducted a screen for microbiome metabolites that would function as inflammasome activators and herein report the identification of 12-oxo-lithocholic acid (BAA485), a potential microbiome-derived bile acid metabolite. We demonstrate that the more potent analogue 11-oxo-12S-hydroxylithocholic acid methyl ester (BAA473) can induce secretion of interleukin-18 (IL-18) through activation of the inflammasome in both myeloid and intestinal epithelial cells. Using a genome-wide CRISPR screen with compound induced pyroptosis in THP-1 cells, we identified that inflammasome activation by BAA473 is pyrin-dependent (MEFV). To our knowledge, the bile acid analogues BAA485 and BAA473 are the first small molecule activators of the pyrin inflammasome. We surmise that pyrin inflammasome activation through microbiota-modified bile acid metabolites such as BAA473 and BAA485 plays a role in gut microbiota regulated intestinal immune response. The discovery of these two bioactive compounds may help to further unveil the importance of pyrin in gut homeostasis and autoimmune diseases.
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Affiliation(s)
- Irina Alimov
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Suchithra Menon
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Nadire Cochran
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Rob Maher
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Qiong Wang
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Alford
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John B Concannon
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Zinger Yang
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Edmund Harrington
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Luis Llamas
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Alicia Lindeman
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Gregory Hoffman
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Tim Schuhmann
- the Novartis Institute for Biomedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Carsten Russ
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - John Reece-Hoyes
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Stephen M Canham
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
| | - Xinming Cai
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139 and
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Proal A, Marshall T. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity. Front Pediatr 2018; 6:373. [PMID: 30564562 PMCID: PMC6288442 DOI: 10.3389/fped.2018.00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.
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Affiliation(s)
- Amy Proal
- Autoimmunity Research Foundation, Thousand Oaks, CA, United States
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Kriaa A, Bourgin M, Potiron A, Mkaouar H, Jablaoui A, Gérard P, Maguin E, Rhimi M. Microbial impact on cholesterol and bile acid metabolism: current status and future prospects. J Lipid Res 2018; 60:323-332. [PMID: 30487175 PMCID: PMC6358303 DOI: 10.1194/jlr.r088989] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/25/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, the gut microbiota has emerged as a crucial factor that influences cholesterol metabolism. Ever since, significant interest has been shown in investigating these host-microbiome interactions to uncover microbiome-mediated functions on cholesterol and bile acid (BA) metabolism. Indeed, changes in gut microbiota composition and, hence, its derived metabolites have been previously reported to subsequently impact the metabolic processes and have been linked to several diseases. In this context, associations between a disrupted gut microbiome, impaired BA metabolism, and cholesterol dysregulation have been highlighted. Extensive advances in metagenomic and metabolomic studies in this field have allowed us to further our understanding of the role of intestinal bacteria in metabolic health and disease. However, only a few have provided mechanistic insights into their impact on cholesterol metabolism. Identifying the myriad functions and interactions of these bacteria to maintain cholesterol homeostasis remain an important challenge in such a field of research. In this review, we discuss the impact of gut microbiota on cholesterol metabolism, its association with disease settings, and the potential of modulating gut microbiota as a promising therapeutic target to lower hypercholesterolemia.
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Affiliation(s)
- Aicha Kriaa
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Mélanie Bourgin
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Aline Potiron
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Héla Mkaouar
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Amin Jablaoui
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Philippe Gérard
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Emmanuelle Maguin
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Moez Rhimi
- UMR 1319 Micalis, INRA, Microbiota Interaction with Human and Animal Team (MIHA), AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
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166
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Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO. Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 2018; 14:e1007735. [PMID: 30399141 PMCID: PMC6219761 DOI: 10.1371/journal.pgen.1007735] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023] Open
Abstract
Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.
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Affiliation(s)
- Wen C. Aw
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard G. Melvin
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Neil A. Youngson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Michael R. Garvin
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Yifang Hu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Center, The University of New South Wales, Sydney, NSW, Australia
| | - Antón Vila-Sanjurjo
- Grupo GIBE, Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña (UDC), Campus Zapateira s/n, A Coruña, Spain
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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