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The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis. Nat Commun 2022; 13:6068. [PMID: 36241650 PMCID: PMC9568547 DOI: 10.1038/s41467-022-33609-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Diurnal (i.e., 24-hour) oscillations of the gut microbiome have been described in various species including mice and humans. However, the driving force behind these rhythms remains less clear. In this study, we differentiate between endogenous and exogenous time cues driving microbial rhythms. Our results demonstrate that fecal microbial oscillations are maintained in mice kept in the absence of light, supporting a role of the host's circadian system rather than representing a diurnal response to environmental changes. Intestinal epithelial cell-specific ablation of the core clock gene Bmal1 disrupts rhythmicity of microbiota. Targeted metabolomics functionally link intestinal clock-controlled bacteria to microbial-derived products, in particular branched-chain fatty acids and secondary bile acids. Microbiota transfer from intestinal clock-deficient mice into germ-free mice altered intestinal gene expression, enhanced lymphoid organ weights and suppressed immune cell recruitment. These results highlight the importance of functional intestinal clocks for microbiota composition and function, which is required to balance the host's gastrointestinal homeostasis.
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Penney NC, Yeung DKT, Garcia-Perez I, Posma JM, Kopytek A, Garratt B, Ashrafian H, Frost G, Marchesi JR, Purkayastha S, Hoyles L, Darzi A, Holmes E. Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity. COMMUNICATIONS MEDICINE 2022; 2:127. [PMID: 36217535 PMCID: PMC9546886 DOI: 10.1038/s43856-022-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
Background Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated. Methods To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (n = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; n = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level. Results Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control. Conclusion We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.
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Affiliation(s)
- Nicholas C. Penney
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
| | - Derek K. T. Yeung
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
| | - Isabel Garcia-Perez
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
| | - Joram M. Posma
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Health Data Research UK, London, NW1 2BE UK
| | - Aleksandra Kopytek
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
| | - Bethany Garratt
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
| | - Hutan Ashrafian
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
| | - Gary Frost
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
| | - Julian R. Marchesi
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
| | - Sanjay Purkayastha
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
| | - Lesley Hoyles
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS UK
| | - Ara Darzi
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, W2 1NY UK
- Institute of Global Health Innovation, Imperial College London, London, W2 1NY UK
| | - Elaine Holmes
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, SW7 2AZ UK
- Centre for Computational & Systems Medicine, Health Futures Institute, Murdoch University, Perth, WA 6150 Australia
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53
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Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle. PLoS Biol 2022; 20:e3001743. [PMID: 36126044 PMCID: PMC9488797 DOI: 10.1371/journal.pbio.3001743] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/06/2022] [Indexed: 12/17/2022] Open
Abstract
The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiota to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure, and respiratory quotient using a novel isolator-housed metabolic cage system, which allows long-term measurements without contamination risk. This demonstrated that microbiota-released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and GF mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well integrated into appetite control. We also observed no significant difference in energy expenditure after normalization by lean mass between the different microbiota groups, suggesting that cumulative small differences in energy balance, or altered energy storage, must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: In GF mice, the respiratory exchange ratio (RER) was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly, the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied GF mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a GF-like drop in liver glycogen storage during the light phase and both liver and plasma metabolomes of OligoMM12 mice clustered closely with GF mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle and which are absent in the OligoMM12 consortium.
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Zarei I, Koistinen VM, Kokla M, Klåvus A, Babu AF, Lehtonen M, Auriola S, Hanhineva K. Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition. Sci Rep 2022; 12:15018. [PMID: 36056162 PMCID: PMC9440220 DOI: 10.1038/s41598-022-19327-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 08/29/2022] [Indexed: 12/13/2022] Open
Abstract
The essential role of gut microbiota in health and disease is well recognized, but the biochemical details that underlie the beneficial impact remain largely undefined. To maintain its stability, microbiota participates in an interactive host-microbiota metabolic signaling, impacting metabolic phenotypes of the host. Dysbiosis of microbiota results in alteration of certain microbial and host metabolites. Identifying these markers could enhance early detection of certain diseases. We report LC-MS based non-targeted metabolic profiling that demonstrates a large effect of gut microbiota on mammalian tissue metabolites. It was hypothesized that gut microbiota influences the overall biochemistry of host metabolome and this effect is tissue-specific. Thirteen different tissues from germ-free (GF) and conventionally-raised (MPF) C57BL/6NTac mice were selected and their metabolic differences were analyzed. Our study demonstrated a large effect of microbiota on mammalian biochemistry at different tissues and resulted in statistically-significant modulation of metabolites from multiple metabolic pathways (p ≤ 0.05). Hundreds of molecular features were detected exclusively in one mouse group, with the majority of these being unique to specific tissue. A vast metabolic response of host to metabolites generated by the microbiota was observed, suggesting gut microbiota has a direct impact on host metabolism.
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Affiliation(s)
- Iman Zarei
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Ville M Koistinen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Itäinen Pitkäkatu 4, 20014, Turku, Finland
| | - Marietta Kokla
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Ambrin Farizah Babu
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, 70211, Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, 70211, Kuopio, Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Itäinen Pitkäkatu 4, 20014, Turku, Finland.
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Martin FP, Tytgat HLP, Krogh Pedersen H, Moine D, Eklund AC, Berger B, Sprenger N. Host-microbial co-metabolites modulated by human milk oligosaccharides relate to reduced risk of respiratory tract infections. Front Nutr 2022; 9:935711. [PMID: 35990340 PMCID: PMC9386273 DOI: 10.3389/fnut.2022.935711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
Human milk oligosaccharides (HMOs) are structurally diverse oligosaccharides present in breast milk, supporting the development of the gut microbiota and immune system. Previously, 2-HMO (2'fucosyllactose, lacto-N-neotetraose) compared to control formula feeding was associated with reduced risk of lower respiratory tract infections (LRTIs), in part linked to lower acetate and higher bifidobacteria proportions. Here, our objective was to gain further insight into additional molecular pathways linking the 2-HMO formula feeding and LRTI mitigation. From the same trial, we measured the microbiota composition and 743 known biochemical species in infant stool at 3 months of age using shotgun metagenomic sequencing and untargeted mass spectrometry metabolomics. We used multivariate analysis to identify biochemicals associated to 2-HMO formula feeding and LRTI and integrated those findings with the microbiota compositional data. Three molecular pathways stood out: increased gamma-glutamylation and N-acetylation of amino acids and decreased inflammatory signaling lipids. Integration of stool metagenomic data revealed some Bifidobacterium and Bacteroides species to be implicated. These findings deepen our understanding of the infant gut/microbiome co-metabolism in early life and provide evidence for how such metabolic changes may influence immune competence at distant mucosal sites such as the airways.
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Affiliation(s)
- François-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Hanne L P Tytgat
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Deborah Moine
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Bernard Berger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Norbert Sprenger
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
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Liaqat H, Parveen A, Kim SY. Neuroprotective Natural Products’ Regulatory Effects on Depression via Gut–Brain Axis Targeting Tryptophan. Nutrients 2022; 14:nu14163270. [PMID: 36014776 PMCID: PMC9413544 DOI: 10.3390/nu14163270] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/23/2022] Open
Abstract
L-tryptophan (Trp) contributes to regulating bilateral communication of the gut–brain axis. It undergoes three major metabolic pathways, which lead to formation of kynurenine, serotonin (5-HT), and indole derivatives (under the control of the microbiota). Metabolites from the principal Trp pathway, kynurenic acid and quinolinic acid, exhibit neuroprotective activity, while picolinic acid exhibits antioxidant activity, and 5-HT modulates appetite, sleep cycle, and pain. Abnormality in Trp plays crucial roles in diseases, including depression, colitis, ulcer, and gut microbiota-related dysfunctions. To address these diseases, the use of natural products could be a favorable alternative because they are a rich source of compounds that can modulate the activity of Trp and combat various diseases through modulating different signaling pathways, including the gut microbiota, kynurenine pathway, and serotonin pathway. Alterations in the signaling cascade pathways via different phytochemicals may help us explore the deep relationships of the gut–brain axis to study neuroprotection. This review highlights the roles of natural products and their metabolites targeting Trp in different diseases. Additionally, the role of Trp metabolites in the regulation of neuroprotective and gastroprotective activities is discussed. This study compiles the literature on novel, potent neuroprotective agents and their action mechanisms in the gut–brain axis and proposes prospective future studies to identify more pharmaceuticals based on signaling pathways targeting Trp.
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Affiliation(s)
- Humna Liaqat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domzale, Slovenia
| | - Amna Parveen
- College of Pharmacy, Gachon University Medical Campus, No. 191, Hambakmoero, Yeonsu-gu, Incheon 21936, Korea
- Correspondence: or (A.P.); (S.Y.K.)
| | - Sun Yeou Kim
- College of Pharmacy, Gachon University Medical Campus, No. 191, Hambakmoero, Yeonsu-gu, Incheon 21936, Korea
- Correspondence: or (A.P.); (S.Y.K.)
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57
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Clerbaux LA, Albertini MC, Amigó N, Beronius A, Bezemer GFG, Coecke S, Daskalopoulos EP, del Giudice G, Greco D, Grenga L, Mantovani A, Muñoz A, Omeragic E, Parissis N, Petrillo M, Saarimäki LA, Soares H, Sullivan K, Landesmann B. Factors Modulating COVID-19: A Mechanistic Understanding Based on the Adverse Outcome Pathway Framework. J Clin Med 2022; 11:4464. [PMID: 35956081 PMCID: PMC9369763 DOI: 10.3390/jcm11154464] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
Addressing factors modulating COVID-19 is crucial since abundant clinical evidence shows that outcomes are markedly heterogeneous between patients. This requires identifying the factors and understanding how they mechanistically influence COVID-19. Here, we describe how eleven selected factors (age, sex, genetic factors, lipid disorders, heart failure, gut dysbiosis, diet, vitamin D deficiency, air pollution and exposure to chemicals) influence COVID-19 by applying the Adverse Outcome Pathway (AOP), which is well-established in regulatory toxicology. This framework aims to model the sequence of events leading to an adverse health outcome. Several linear AOPs depicting pathways from the binding of the virus to ACE2 up to clinical outcomes observed in COVID-19 have been developed and integrated into a network offering a unique overview of the mechanisms underlying the disease. As SARS-CoV-2 infectibility and ACE2 activity are the major starting points and inflammatory response is central in the development of COVID-19, we evaluated how those eleven intrinsic and extrinsic factors modulate those processes impacting clinical outcomes. Applying this AOP-aligned approach enables the identification of current knowledge gaps orientating for further research and allows to propose biomarkers to identify of high-risk patients. This approach also facilitates expertise synergy from different disciplines to address public health issues.
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Affiliation(s)
- Laure-Alix Clerbaux
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | | | - Núria Amigó
- Biosfer Teslab SL., 43204 Reus, Spain;
- Department of Basic Medical Sciences, Universitat Rovira i Virgili (URV), 23204 Reus, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Gillina F. G. Bezemer
- Impact Station, 1223 JR Hilversum, The Netherlands;
- Department of Pharmaceutical Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sandra Coecke
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Evangelos P. Daskalopoulos
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Ceze, France;
| | - Alberto Mantovani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium;
| | - Elma Omeragic
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Nikolaos Parissis
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Laura A. Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Helena Soares
- Laboratory of Immunobiology and Pathogenesis, Chronic Diseases Research Centre, Faculdade de Ciências Médicas Medical School, University of Lisbon, 1649-004 Lisbon, Portugal;
| | - Kristie Sullivan
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA;
| | - Brigitte Landesmann
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
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Duszka K. Versatile Triad Alliance: Bile Acid, Taurine and Microbiota. Cells 2022; 11:2337. [PMID: 35954180 PMCID: PMC9367564 DOI: 10.3390/cells11152337] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/21/2022] Open
Abstract
Taurine is the most abundant free amino acid in the body, and is mainly derived from the diet, but can also be produced endogenously from cysteine. It plays multiple essential roles in the body, including development, energy production, osmoregulation, prevention of oxidative stress, and inflammation. Taurine is also crucial as a molecule used to conjugate bile acids (BAs). In the gastrointestinal tract, BAs deconjugation by enteric bacteria results in high levels of unconjugated BAs and free taurine. Depending on conjugation status and other bacterial modifications, BAs constitute a pool of related but highly diverse molecules, each with different properties concerning solubility and toxicity, capacity to activate or inhibit receptors of BAs, and direct and indirect impact on microbiota and the host, whereas free taurine has a largely protective impact on the host, serves as a source of energy for microbiota, regulates bacterial colonization and defends from pathogens. Several remarkable examples of the interaction between taurine and gut microbiota have recently been described. This review will introduce the necessary background information and lay out the latest discoveries in the interaction of the co-reliant triad of BAs, taurine, and microbiota.
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Affiliation(s)
- Kalina Duszka
- Department of Nutritional Sciences, University of Vienna, 1090 Vienna, Austria
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59
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Vieira V, Ferreira J, Rocha M. A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. PLoS Comput Biol 2022; 18:e1009294. [PMID: 35749559 PMCID: PMC9278738 DOI: 10.1371/journal.pcbi.1009294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/13/2022] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
Constraint-based (CB) metabolic models provide a mathematical framework and scaffold for in silico cell metabolism analysis and manipulation. In the past decade, significant efforts have been done to model human metabolism, enabled by the increased availability of multi-omics datasets and curated genome-scale reconstructions, as well as the development of several algorithms for context-specific model (CSM) reconstruction. Although CSM reconstruction has revealed insights on the deregulated metabolism of several pathologies, the process of reconstructing representative models of human tissues still lacks benchmarks and appropriate integrated software frameworks, since many tools required for this process are still disperse across various software platforms, some of which are proprietary. In this work, we address this challenge by assembling a scalable CSM reconstruction pipeline capable of integrating transcriptomics data in CB models. We combined omics preprocessing methods inspired by previous efforts with in-house implementations of existing CSM algorithms and new model refinement and validation routines, all implemented in the Troppo Python-based open-source framework. The pipeline was validated with multi-omics datasets from the Cancer Cell Line Encyclopedia (CCLE), also including reference fluxomics measurements for the MCF7 cell line. We reconstructed over 6000 models based on the Human-GEM template model for 733 cell lines featured in the CCLE, using MCF7 models as reference to find the best parameter combinations. These reference models outperform earlier studies using the same template by comparing gene essentiality and fluxomics experiments. We also analysed the heterogeneity of breast cancer cell lines, identifying key changes in metabolism related to cancer aggressiveness. Despite the many challenges in CB modelling, we demonstrate using our pipeline that combining transcriptomics data in metabolic models can be used to investigate key metabolic shifts. Significant limitations were found on these models ability for reliable quantitative flux prediction, thus motivating further work in genome-wide phenotype prediction. Genome-scale models of human metabolism are promising tools capable of contextualising large omics datasets within a framework that enables analysis and manipulation of metabolic phenotypes. Despite various successes in applying these methods to provide mechanistic hypotheses for deregulated metabolism in disease, there is no standardized workflow to extract these models using existing methods and the tools required to do so are mostly implemented using proprietary software. We have assembled a generic pipeline to extract and validate context-specific metabolic models using multi-omics datasets and implemented it using the troppo framework. We first validate our pipeline using MCF7 cell line models and assess their ability to predict lethal gene knockouts as well as flux activity using multi-omics data. We also demonstrate how this approach can be generalized for large-scale transcriptomics datasets and used to generate insights on the metabolic heterogeneity of cancer and relevant features for other data mining approaches. The pipeline is available as part of an open-source framework that is generic for a variety of applications.
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Affiliation(s)
- Vítor Vieira
- Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal
| | - Jorge Ferreira
- Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
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60
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Gnainsky Y, Itkin M, Mehlman T, Brandis A, Malitsky S, Soen Y. Protocol for studying microbiome impact on host energy and reproduction in Drosophila. STAR Protoc 2022; 3:101253. [PMID: 35330965 PMCID: PMC8938908 DOI: 10.1016/j.xpro.2022.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Drosophila gut microbiome in flies has been shown to have a systemic influence on energy production by the host and the energetic investment in growth and reproduction. Here we describe a protocol for studying the mechanisms responsible for this remote regulation by gut bacteria. This protocol enables whole-body and ovary-specific quantification of energy-storing molecules as well as identification of host metabolites and pathways that are regulated by gut microbiome-derived factors. Similar procedures are applicable to additional treatments and genetic manipulations. For complete details on the use and execution of this protocol, please refer to Gnainsky et al. (2021). Protocol for studying Drosophila gut bacteria impact on host metabolism and reproduction Preparation of germ-free flies and evaluation of oocyte development An assay for sensitive detection and quantification of energy-storing molecules Metabolomic analysis and identification of altered metabolic pathways
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Affiliation(s)
- Yulia Gnainsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7670001, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7670001, Israel
| | - Tevie Mehlman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7670001, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7670001, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7670001, Israel
| | - Yoav Soen
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7670001, Israel
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Wang S, Chen H, Yang H, Zhou K, Bai F, Wu X, Xu H. Gut Microbiome Was Highly Related to the Regulation of Metabolism in Lung Adenocarcinoma Patients. Front Oncol 2022; 12:790467. [PMID: 35592677 PMCID: PMC9113755 DOI: 10.3389/fonc.2022.790467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/21/2022] [Indexed: 11/27/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is one of the most predominant subtypes of lung cancer. The gut microbiome plays a vital role in the pathophysiological processes of various diseases, including cancers. Methods In the study, 100 individuals were enrolled. In total 75 stool and blood samples were analyzed with 16s-rRNA gene sequencing and metabolomics (30 from healthy individuals (H); 45 from LUAD patients). In addition, 25 stool samples were analyzed with metagenomics (10 from H; 15 from LUAD). The linear discriminant analysis (LDA) effect size (LefSe) and logistic regression analysis were applied to identify biomarkers’ taxa and develop a diagnostic model. The diagnostic power of the model was estimated with the receiver operating characteristic curve (ROC) by comparing the area under the ROC (AUC). The correlation between biomarker’s taxa and metabolites was calculated using the Spearman analysis. Results The α and β diversity demonstrated the composition and structure of the gut microbiome in LUAD patients were different from those in healthy people. The top three abundance of genera were Bacteroides (25.06%), Faecalibacterium (11.00%), and Prevotella (5.94%). The LefSe and logistic regression analysis identified three biomarker taxa (Bacteroides, Pseudomonas, and Ruminococcus gnavus group) and constructed a diagnostic model. The AUCs of the diagnostic model in 16s-rRNA gene sequencing and metagenomics were 0.852 and 0.841, respectively. A total of 102 plasma metabolites were highly related to those three biomarkers’ taxa. Seven metabolic pathways were enriched by 102 plasma metabolites, including the Pentose phosphate pathway, Glutathione metabolism. Conclusions In LUAD patients, the gut microbiome profile has significantly changed. We used three biomarkers taxa to develop a diagnostic model, which was accurate and suitable for the diagnosis of LUAD. Gut microbes, especially those three biomarkers’ taxa, may participate in regulating metabolism-related pathways in LUAD patients, such as the pentose phosphate pathway and glutathione metabolism.
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Affiliation(s)
- Sheng Wang
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Huachun Chen
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Huizhen Yang
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Kejin Zhou
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Fan Bai
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Xiaoyu Wu
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
| | - Hanwen Xu
- Department of Respiratory, Jinhua Guangfu Hospital, Jinhua, China
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Naya-Català F, Piazzon MC, Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream. Front Microbiol 2022; 13:883738. [PMID: 35602034 PMCID: PMC9121002 DOI: 10.3389/fmicb.2022.883738] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is now recognised as a key target for improving aquaculture profit and sustainability, but we still lack insights into the activity of microbes in fish mucosal surfaces. In the present study, a metatranscriptomic approach was used to reveal the expression of gut microbial genes in the farmed gilthead sea bream. Archaeal and viral transcripts were a minority but, interestingly and contrary to rRNA amplicon-based studies, fungal transcripts were as abundant as bacterial ones, and increased in fish fed a plant-enriched diet. This dietary intervention also drove a differential metatranscriptome in fish selected for fast and slow growth. Such differential response reinforced the results of previously inferred metabolic pathways, enlarging, at the same time, the catalogue of microbial functions in the intestine. Accordingly, vitamin and amino acid metabolism, and rhythmic and symbiotic processes were mostly shaped by bacteria, whereas fungi were more specifically configuring the host immune, digestive, or endocrine processes.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - M. Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
- M. Carla Piazzon,
| | - Josep A. Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal Spanish National Research Council (IATS-CSIC), Valencia, Spain
- *Correspondence: Jaume Pérez-Sánchez,
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Song BS, Moon JS, Tian J, Lee HY, Sim BC, Kim SH, Kang SG, Kim JT, Nga HT, Benfeitas R, Kim Y, Park S, Wolfe RR, Eun HS, Shong M, Lee S, Kim IY, Yi HS. Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion. J Immunother Cancer 2022; 10:jitc-2021-004337. [PMID: 35580931 PMCID: PMC9114962 DOI: 10.1136/jitc-2021-004337] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Mitochondria are involved in cancer energy metabolism, although the mechanisms underlying the involvement of mitoribosomal dysfunction in hepatocellular carcinoma (HCC) remain poorly understood. Here, we investigated the effects of mitoribosomal impairment-mediated alterations on the immunometabolic characteristics of liver cancer. METHODS We used a mouse model of HCC, liver tissues from patients with HCC, and datasets from The Cancer Genome Atlas (TCGA) to elucidate the relationship between mitoribosomal proteins (MRPs) and HCC. In a mouse model, we selectively disrupted expression of the mitochondrial ribosomal protein CR6-interacting factor 1 (CRIF1) in hepatocytes to determine the impact of hepatocyte-specific impairment of mitoribosomal function on liver cancer progression. The metabolism and immunophenotype of liver cancer was assessed by glucose flux assays and flow cytometry, respectively. RESULTS Single-cell RNA-seq analysis of tumor tissue and TCGA HCC transcriptome analysis identified mitochondrial defects associated with high-MRP expression and poor survival outcomes. In the mouse model, hepatocyte-specific disruption of the mitochondrial ribosomal protein CRIF1 revealed the impact of mitoribosomal dysfunction on liver cancer progression. Crif1 deficiency promoted programmed cell death protein 1 expression by immune cells in the hepatic tumor microenvironment. A [U-13C6]-glucose tracer demonstrated enhanced glucose entry into the tricarboxylic acid cycle and lactate production in mice with mitoribosomal defects during cancer progression. Mice with hepatic mitoribosomal defects also exhibited enhanced progression of liver cancer accompanied by highly exhausted tumor-infiltrating T cells. Crif1 deficiency induced an environment unfavorable to T cells, leading to exhaustion of T cells via elevation of reactive oxygen species and lactate production. CONCLUSIONS Hepatic mitoribosomal defects promote glucose partitioning toward glycolytic flux and lactate synthesis, leading to T cell exhaustion and cancer progression. Overall, the results suggest a distinct role for mitoribosomes in regulating the immunometabolic microenvironment during HCC progression.
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Affiliation(s)
- Byong-Sop Song
- Department of Core Laboratory of Translational Research, Biomedical Convergence Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | - Ji Sun Moon
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Jingwen Tian
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Ho Yeop Lee
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Byeong Chang Sim
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Seok-Hwan Kim
- Department of Surgery, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Seul Gi Kang
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Jung Tae Kim
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Ha Thi Nga
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Stockholm, Sweden
| | - Yeongmin Kim
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Incheon, South Korea
| | - Sanghee Park
- Department of Molecular Medicine, College of Medicine, Gachon University, Incheon, South Korea
| | - Robert R Wolfe
- Department of Geriatrics, the Center for Translational Research in Aging & Longevity, Donald W. Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Hyuk Soo Eun
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Minho Shong
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Sunjae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Il-Young Kim
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology (GAIHST), Incheon, South Korea .,Department of Molecular Medicine, College of Medicine, Gachon University, Incheon, South Korea
| | - Hyon-Seung Yi
- Department of Core Laboratory of Translational Research, Biomedical Convergence Research Center, Chungnam National University Hospital, Daejeon, South Korea .,Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon, South Korea.,Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
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Jiang SQ, Pan T, Yu JL, Zhang Y, Wang T, Li P, Li F. Thermal and wine processing enhanced Clematidis Radix et Rhizoma ameliorate collagen Ⅱ induced rheumatoid arthritis in rats. JOURNAL OF ETHNOPHARMACOLOGY 2022; 288:114993. [PMID: 35032583 DOI: 10.1016/j.jep.2022.114993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Clematidis Radix et Rhizoma, a kind of traditional Chinese medicine, is derived from Clematis chinensis Osbeck, Clematis hexapetala Pall. and Clematis manshurica Rupr. This herb shows great effects on expelling wind and dispelling dampness in ancient and it has anti-inflammatory and analgesic activity in modern clinical application. AIM OF THE STUDY This experiment aimed to research anti-rheumatoid arthritis effect of crude and wine processed RC based on glycolysis metabolism to provide new ideas treating RA. MATERIALS AND METHODS Network pharmacology was applied to preliminarily forecast the potential pathways of common targets of RC and RA. RAW264.7 macrophages were induced by LPS, NO production, glucose uptake, lactate production, ROS and MMP were detected as instructions in vitro. ELISA was used to measure the content of HK2, PKM2 and LDHA involving in glycolysis process. Gut microbiota was analyzed by 16S rRNA gene amplicon sequencing in CIA rats. RESULTS Crude and wine processed RC had good anti-inflammatory effect by reducing NO in RAW264.7 macrophages and ameliorating inflammatory infiltration and cartilage surface erosion in CIA rats. Whether in LPS-induced macrophages or CIA rats, crude and wine processed RC could inhibit glycolysis by down-regulating the expression of PKM2, causing less glucose uptake and lactic acid, which lead to less ROS and higher MMP to normal. PI3K-AKT and HIF-1α pathways were deduced to possibly play a crucial part in controlling glycolysis metabolism by network pharmacology analysis. Besides, it was displayed that Firmicutes and Bacteroidetes were prominent gut microbiota in CIA rats feces. CC-H and PZ-H groups could both increase the relative abundance of Firmicutes and decrease Bacteroidetes. These microbiota also played a role in RA pathological process via involving in energy metabolism, carbohydrate metabolism and immune system. CONCLUSION Crude and wine processed RC have a good influence in ameliorating rheumatoid arthritis by inhibiting glycolysis and modulating gut microbiota together.
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Affiliation(s)
- Si-Qi Jiang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ting Pan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jia-Lin Yu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ying Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ting Wang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Resource, Yunnan University of Chinese Medicine, Kunming, 650000, PR China.
| | - Ping Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Fei Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China; School of Pharmacy, Xinjiang Medical University, Urumqi, 830011, PR China.
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Hulme H, Meikle LM, Strittmatter N, Swales J, Hamm G, Brown SL, Milling S, MacDonald AS, Goodwin RJ, Burchmore R, Wall DM. Mapping the Influence of the Gut Microbiota on Small Molecules across the Microbiome Gut Brain Axis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:649-659. [PMID: 35262356 PMCID: PMC9047441 DOI: 10.1021/jasms.1c00298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Microbes exert influence across the microbiome-gut-brain axis through neurotransmitter production, induction of host immunomodulators, or the release or induction of other microbial or host molecules. Here, we used mass spectrometry imaging (MSI), a label-free imaging tool, to map molecular changes in the gut and brain in germ-free, antibiotic-treated and control mice. We determined spatial distribution and relative quantification of neurotransmitters and their precursors in response to the microbiome. Using untargeted MSI, we detected a significant change in the levels of four identified small molecules in the brains of germ-free animals compared to controls. However, antibiotic treatment induced no significant changes in these same metabolites in the brain after 1 week of treatment. This work exemplifies the utility of MSI as a tool for the study of known and discovery of novel, mediators of microbiome-gut-brain axis communication.
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Affiliation(s)
- Heather Hulme
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Lynsey M. Meikle
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Nicole Strittmatter
- Imaging
and Data Analytics, Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - John Swales
- Imaging
and Data Analytics, Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Gregory Hamm
- Imaging
and Data Analytics, Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Sheila L. Brown
- Lydia
Becker Institute of Immunology and Inflammation, Faculty of Biology,
Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, U.K.
| | - Simon Milling
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Andrew S. MacDonald
- Lydia
Becker Institute of Immunology and Inflammation, Faculty of Biology,
Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, U.K.
| | - Richard J.A. Goodwin
- Imaging
and Data Analytics, Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Richard Burchmore
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Daniel M. Wall
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, United Kingdom
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66
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Zhou Z, Wu H, Li D, Zeng W, Huang J, Wu Z. Comparison of gut microbiome in the Chinese mud snail ( Cipangopaludina chinensis) and the invasive golden apple snail ( Pomacea canaliculata). PeerJ 2022; 10:e13245. [PMID: 35402093 PMCID: PMC8992660 DOI: 10.7717/peerj.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
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Affiliation(s)
- Zihao Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Hongying Wu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Dinghong Li
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Wenlong Zeng
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China,College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
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67
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Selway CA, Sudarpa J, Weyrich LS. Moving beyond the gut microbiome: combining systems biology and multi-site microbiome analyses to combat non-communicable diseases. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Gut Microbiome in Non-Alcoholic Fatty Liver Disease: From Mechanisms to Therapeutic Role. Biomedicines 2022; 10:biomedicines10030550. [PMID: 35327352 PMCID: PMC8945462 DOI: 10.3390/biomedicines10030550] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is considered to be a significant health threat globally, and has attracted growing concern in the research field of liver diseases. NAFLD comprises multifarious fatty degenerative disorders in the liver, including simple steatosis, steatohepatitis and fibrosis. The fundamental pathophysiology of NAFLD is complex and multifactor-driven. In addition to viruses, metabolic syndrome and alcohol, evidence has recently indicated that the microbiome is related to the development and progression of NAFLD. In this review, we summarize the possible microbiota-based therapeutic approaches and highlight the importance of establishing the diagnosis of NAFLD through the different spectra of the disease via the gut–liver axis.
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69
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Population Genomics, Transcriptional Response to Heat Shock, and Gut Microbiota of the Hong Kong Oyster Magallana hongkongensis. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species native to the estuarine-coast of the Pearl River Delta in southern China. The species—with scientific, ecological, cultural, and nutritional importance—has been farmed for hundreds of years. However, there is only limited information on its genetics, stress adaptation mechanisms, and gut microbiota, restricting the sustainable production and use of oyster resources. Here, we present population structure analysis on M. hongkongensis oysters collected from Deep Bay and Lantau Island in Hong Kong, as well as transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis oysters collected from Deep Bay. Single nucleotide polymorphisms (SNPs), including those on the homeobox genes and heat shock protein genes, were revealed by the whole genome resequencing. Transcriptomes of oysters incubated at 25 °C and 32 °C for 24 h were sequenced which revealed the heat-induced regulation of heat shock protein pathway genes. Furthermore, the gut microbe community was detected by 16S rRNA sequencing which identified Cyanobacteria, Proteobacteria and Spirochaetes as the most abundant phyla. This study reveals the molecular basis for the adaptation of the oyster M. hongkongensis to environmental conditions.
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70
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Pessa-Morikawa T, Husso A, Kärkkäinen O, Koistinen V, Hanhineva K, Iivanainen A, Niku M. Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. BMC Microbiol 2022; 22:46. [PMID: 35130835 PMCID: PMC8819883 DOI: 10.1186/s12866-022-02457-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/29/2022] [Indexed: 12/20/2022] Open
Abstract
Background The maternal microbiota affects the development of the offspring by microbial metabolites translocating to the fetus. To reveal the spectrum of these molecular mediators of the earliest host-microbe interactions, we compared placenta, fetal intestine and brain from germ-free (GF) and specific pathogen free (SPF) mouse dams by non-targeted metabolic profiling. Results One hundred one annotated metabolites and altogether 3680 molecular features were present in significantly different amounts in the placenta and/or fetal organs of GF and SPF mice. More than half of these were more abundant in the SPF organs, suggesting their microbial origin or a metabolic response of the host to the presence of microbes. The clearest separation was observed in the placenta, but most of the molecular features showed significantly different levels also in the fetal intestine and/or brain. Metabolites that were detected in lower amounts in the GF fetal organs included 5-aminovaleric acid betaine, trimethylamine N-oxide, catechol-O-sulphate, hippuric and pipecolic acid. Derivatives of the amino acid tryptophan, such as kynurenine, 3-indolepropionic acid and hydroxyindoleacetic acid, were also less abundant in the absence of microbiota. Ninety-nine molecular features were detected only in the SPF mice. We also observed several molecular features which were more abundant in the GF mice, possibly representing precursors of microbial metabolites or indicators of a metabolic response to the absence of microbiota. Conclusions The maternal microbiota has a profound impact on the fetal metabolome. Our observations suggest the existence of a multitude of yet unidentified microbially modified metabolites which pass through the placenta into the fetus and potentially influence fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02457-6.
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Affiliation(s)
- Tiina Pessa-Morikawa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Aleksi Husso
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Kärkkäinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland.,Afekta Technologies Ltd., Kuopio, Finland
| | - Ville Koistinen
- Afekta Technologies Ltd., Kuopio, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Food Chemistry and Food Development Unit, University of Turku, Turku, Finland
| | - Kati Hanhineva
- Afekta Technologies Ltd., Kuopio, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Food Chemistry and Food Development Unit, University of Turku, Turku, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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Gregor A, Pignitter M, Trajanoski S, Auernigg-Haselmaier S, Somoza V, König J, Duszka K. Microbial contribution to the caloric restriction-triggered regulation of the intestinal levels of glutathione transferases, taurine, and bile acid. Gut Microbes 2022; 13:1992236. [PMID: 34693866 PMCID: PMC8547879 DOI: 10.1080/19490976.2021.1992236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recently we showed that caloric restriction (CR) triggers an increase in the levels of free taurine, taurine-conjugated bile acids (BA), and other taurine conjugates in intestinal mucosa while decreasing glutathione (GSH) levels in wild-type male mice. In the current project, we decided to investigate whether the microbiota is involved in the response to CR by depleting gut bacteria. The antibiotics treatment diminished CR-specific increase in the levels of free taurine and its conjugates as well as upregulated expression and activity of GSH transferases (GST) in the intestinal mucosa. Further, it diminished a CR-related increase in BAs levels in the liver, plasma, and intestinal mucosa. Transplant of microbiota from CR mice to ad libitum fed mice triggered CR-like changes in MGST1 expression, levels of taurine and taurine conjugates in the mucosa of the ileum. We show for the first time, that microbiota contributes to the intestinal response to CR-triggered changes in BA, taurine, and GST levels.
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Affiliation(s)
- András Gregor
- Department of Nutritional Sciences, University of Vienna, Vienna, Austria
| | - Marc Pignitter
- Department of Physiological Chemistry, University of Vienna, Vienna, Austria
| | - Slave Trajanoski
- Core Facility Computational Bioanalytics, Medical University of Graz, Graz, Austria
| | | | - Veronika Somoza
- Department of Physiological Chemistry, University of Vienna, Vienna, Austria,Leibniz-Institut for Food Systems Biology, Technical University of Munich, Munich, Germany
| | - Jürgen König
- Department of Nutritional Sciences, University of Vienna, Vienna, Austria
| | - Kalina Duszka
- Department of Nutritional Sciences, University of Vienna, Vienna, Austria,CONTACT Kalina Duszka Department of Nutritional Sciences, University of Vienna, Vienna, Austria
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72
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Yin H, Zhong Y, Wang H, Hu J, Xia S, Xiao Y, Nie S, Xie M. Short-term exposure to high relative humidity increases blood urea and influences colonic urea-nitrogen metabolism by altering the gut microbiota. J Adv Res 2022; 35:153-168. [PMID: 35003799 PMCID: PMC8721250 DOI: 10.1016/j.jare.2021.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 01/20/2023] Open
Abstract
Plasma urea was increased along with erythrocyte Na+/K+ -ATPase activity reduced and abnormal erythrocyte morphologies appeared during 14-day high relative humidity (90 ± 2%) exposure. Shortly after 12-h and 24-h exposures, urea influx and ammonia level were increased in the colon of mice, respectively. Colonic urea-nitrogen metabolism was influenced by the increased levels of ammonia, amino acids and short-chain fatty acids during 14-day exposure. Gut bacteria related to urease production, amino acids metabolism and SCFAs production was enriched during the exposure.
Introduction Colonic urea-nitrogen metabolites have been implicated in the pathogenesis of certain diseases which can be affected by environmental factors. Objectives We aimed to explore the influence of ambient humidity on colonic urea-nitrogen metabolism. Methods Blood biochemical indexes, metabolites of intestinal tract, and gut microbiota composition of mice (n = 10/group) exposed to high relative humidity (RH, 90 ± 2%) were analyzed during the 14-day exposure. Results After 12-h exposure, plasma blood urea nitrogen (BUN) level increased along with a decrease in the activity of erythrocyte Na+/K+ -ATPase. Moreover, abnormal erythrocyte morphologies appeared after 3 days of exposure. The colonic BUN and ammonia levels increased significantly after the 12-h and 24-h exposure, respectively. The colonic level of amino acids, partly synthesized by gut microbiota using ammonia as the nitrogen source, was significantly higher on the 7th day. Furthermore, the level of fecal short-chain fatty acids was significantly higher after 3-day exposure and the level of branched-chain fatty acids increased on the 14th day. Overall, gut microbiota composition was continuously altered during exposure, facilitating the preferential proliferation of urea-nitrogen metabolism bacteria. Conclusion Our findings suggest that short-term high RH exposure influences colonic urea-nitrogen metabolism by increasing the influx of colonic urea and altering gut microbiota, which might further impact the host health outcomes.
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Affiliation(s)
- Hongmei Yin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Yadong Zhong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Jielun Hu
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Shengkun Xia
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Yuandong Xiao
- The College of National Land Resource and Environment, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.,National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
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73
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Song Z, Luo W, Huang B, Cao Y, Jiang R. A new predictive model for the concurrent risk of diabetic retinopathy in type 2 diabetes patients and the effect of metformin on amino acids. Front Endocrinol (Lausanne) 2022; 13:985776. [PMID: 36060930 PMCID: PMC9434554 DOI: 10.3389/fendo.2022.985776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE This study established a model to predict the risk of diabetic retinopathy (DR) with amino acids selected by partial least squares (PLS) method, and evaluated the effect of metformin on the effect of amino acids on DR in the model. METHODS In Jinzhou, Liaoning Province, China, we retrieved 1031 patients with type 2 diabetes (T2D) from the First Affiliated Hospital of Liaoning Medical University. After sorting the amino acids using the PLS method, the top 10 amino acids were included in the model. Multivariate logistic regression was used to analyze the relationship between different amino acids and DR. And then the effects of metformin on amino acids were explored through interaction. Finally, Spearman's rank correlation analysis was used to analyze the correlation between different amino acids. RESULTS After sorting by PLS, Gly, Pro, Leu, Lyr, Glu, Phe, Tyr, His, Val and Ser were finally included in the DR risk prediction model. The predictive model after adding amino acids was statistically different from the model that only included traditional risk factors (p=0.001). Metformin had a significant effect on the relationship between DR and 7 amino acids (Gly, Glu, Phe, Tyr, His, Val, Ser, p<0.05), and the population who are not using metformin and have high levels of Glu (OR: 0.44, 95%CI: 0.27-0.71) had an additive protection effect for the occurrence of DR. And the similar results can be seen in high levels of Gly (OR: 0.46, 95%CI: 0.29-0.75), Leu (OR: 0.48, 95%CI: 0.29-0.8), His (OR: 0.46, 95%CI: 0.29-0.75), Phe (OR: 0.24, 95%CI: 0.14-0.42) and Tyr (OR: 0.41, 95%CI: 0.24 -0.68) in population who are not using metformin. CONCLUSIONS We established a prediction model of DR by amino acids and found that the use of metformin reduced the protective effect of amino acids on DR developing, suggesting that amino acids as biomarkers for predicting DR would be affected by metformin use.
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Affiliation(s)
- Zicheng Song
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Weiming Luo
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Bing Huang
- Research Department, Dalian Innovation Center of Laboratory Medicine Mass Spectrometry Technology, Dalian, China
- Research Department, Clinical Mass Spectrometry Profession Technology Innovation Center of Liaoning Province, Jinzhou, China
- Research Department, Dalian Laboratory Medicine Mass Spectrometry Technology Development Innovation Team, Dalian, China
| | - Yunfeng Cao
- Department of Scientific Research, Shanghai Institute of Planned Parenthood Research, Shanghai, China
- Dalian Institute of Chemical Physics. Chinese Academy of Sciences, Dalian, China
- *Correspondence: Yunfeng Cao, ; Rongzhen Jiang,
| | - Rongzhen Jiang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Yunfeng Cao, ; Rongzhen Jiang,
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74
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Rath E, Haller D. Intestinal epithelial cell metabolism at the interface of microbial dysbiosis and tissue injury. Mucosal Immunol 2022; 15:595-604. [PMID: 35534699 PMCID: PMC9259489 DOI: 10.1038/s41385-022-00514-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 02/07/2023]
Abstract
The intestinal epithelium represents the most regenerative tissue in the human body, located in proximity to the dense and functionally diverse microbial milieu of the microbiome. Episodes of tissue injury and incomplete healing of the intestinal epithelium are a prerequisite for immune reactivation and account for recurrent, chronically progressing phenotypes of inflammatory bowel diseases (IBD). Mitochondrial dysfunction and associated changes in intestinal epithelial functions are emerging concepts in the pathogenesis of IBD, suggesting impaired metabolic flexibility of epithelial cells affects the regenerative capacity of the intestinal tissue. Next to rendering the intestinal mucosa susceptible to inflammatory triggers, metabolic reprogramming of the epithelium is implicated in shaping adverse microbial environments. In this review, we introduce the concept of "metabolic injury" as a cell autonomous mechanism of tissue wounding in response to mitochondrial perturbation. Furthermore, we highlight epithelial metabolism as intersection of microbiome, immune cells and epithelial regeneration.
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Affiliation(s)
- Eva Rath
- grid.6936.a0000000123222966Technical University of Munich, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| | - Dirk Haller
- grid.6936.a0000000123222966Technical University of Munich, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany ,grid.6936.a0000000123222966Technical University of Munich, ZIEL Institute for Food & Health, Freising-Weihenstephan, Germany
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75
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Schiavi S, La Rosa P, Petrillo S, Carbone E, D'Amico J, Piemonte F, Trezza V. N-Acetylcysteine Mitigates Social Dysfunction in a Rat Model of Autism Normalizing Glutathione Imbalance and the Altered Expression of Genes Related to Synaptic Function in Specific Brain Areas. Front Psychiatry 2022; 13:851679. [PMID: 35280167 PMCID: PMC8916240 DOI: 10.3389/fpsyt.2022.851679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
Prenatal exposure to valproic acid (VPA) is a risk factor for autism spectrum disorder (ASD) in humans and it induces autistic-like behaviors in rodents. Imbalances between GABAergic and glutamatergic neurotransmission and increased oxidative stress together with altered glutathione (GSH) metabolism have been hypothesized to play a role in both VPA-induced embriotoxicity and in human ASD. N-acetylcysteine (NAC) is an antioxidant precursor of glutathione and a modulator of glutamatergic neurotransmission that has been tested in ASD, although the clinical studies currently available provided controversial results. Here, we explored the effects of repeated NAC (150 mg/kg) administration on core autistic-like features and altered brain GSH metabolism in the VPA (500 mg/kg) rat model of ASD. Furthermore, we measured the mRNA expression of genes encoding for scaffolding and transcription regulation proteins, as well as the subunits of NMDA and AMPA receptors and metabotropic glutamate receptors mGLUR1 and mGLUR5 in brain areas that are relevant to ASD. NAC administration ameliorated the social deficit displayed by VPA-exposed rats in the three-chamber test, but not their stereotypic behavior in the hole board test. Furthermore, NAC normalized the altered GSH levels displayed by these animals in the hippocampus and nucleus accumbens, and it partially rescued the altered expression of post-synaptic terminal network genes found in VPA-exposed rats, such as NR2a, MGLUR5, GLUR1, and GLUR2 in nucleus accumbens, and CAMK2, NR1, and GLUR2 in cerebellum. These data indicate that NAC treatment selectively mitigates the social dysfunction displayed by VPA-exposed rats normalizing GSH imbalance and reestablishing the expression of genes related to synaptic function in a brain region-specific manner. Taken together, these data contribute to clarify the behavioral impact of NAC in ASD and the molecular mechanisms that underlie its effects.
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Affiliation(s)
- Sara Schiavi
- Department of Science, University "Roma Tre", Rome, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University, Rome, Italy
| | - Sara Petrillo
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emilia Carbone
- Department of Science, University "Roma Tre", Rome, Italy
| | - Jessica D'Amico
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fiorella Piemonte
- Neuromuscular and Neurodegenerative Diseases Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana Trezza
- Department of Science, University "Roma Tre", Rome, Italy
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Wang F, Zou J, Xu H, Huang W, Zhang X, Wei Z, Li X, Liu Y, Zou J, Liu F, Zhu H, Yi H, Guan J, Yin S. Effects of Chronic Intermittent Hypoxia and Chronic Sleep Fragmentation on Gut Microbiome, Serum Metabolome, Liver and Adipose Tissue Morphology. Front Endocrinol (Lausanne) 2022; 13:820939. [PMID: 35178032 PMCID: PMC8846366 DOI: 10.3389/fendo.2022.820939] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/06/2022] [Indexed: 12/29/2022] Open
Abstract
Chronic intermittent hypoxia (CIH) and chronic sleep fragmentation (CSF) are two cardinal pathological features of obstructive sleep apnea (OSA). Dietary obesity is a crucial risk intermediator for OSA and metabolic disorders. Gut microbiota affect hepatic and adipose tissue morphology under conditions of CIH or CSF through downstream metabolites. However, the exact relationship is unclear. Herein, chow and high-fat diet (HFD)-fed mice were subjected to CIH or CSF for 10 weeks each and compared to normoxia (NM) or normal sleep (NS) controls. 16S rRNA amplicon sequencing, untargeted liquid chromatography-tandem mass spectrometry, and histological assessment of liver and adipose tissues were used to investigate the correlations between the microbiome, metabolome, and lipid metabolism under CIH or CSF condition. Our results demonstrated that CIH and CSF regulate the abundance of intestinal microbes (such as Akkermansia mucinphila, Clostridium spp., Lactococcus spp., and Bifidobacterium spp.) and functional metabolites, such as tryptophan, free fatty acids, branched amino acids, and bile acids, which influence adipose tissue and hepatic lipid metabolism, and the level of lipid deposition in tissues and peripheral blood. In conclusion, CIH and CSF adversely affect fecal microbiota composition and function, and host metabolism; these findings provide new insight into the independent and synergistic effects of CIH, CSF, and HFD on lipid disorders.
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Affiliation(s)
- Fan Wang
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Juanjuan Zou
- Department of Otorhinolaryngology and National Health Commission (NHC) Key Laboratory of Otorhinolaryngology, Shandong University Affiliated Qilu Hospital, Jinan, China
| | - Huajun Xu
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Huajun Xu, ; Jian Guan, ; Shankai Yin,
| | - Weijun Huang
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaoman Zhang
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Zhicheng Wei
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xinyi Li
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Yupu Liu
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jianyin Zou
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Feng Liu
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Huaming Zhu
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Hongliang Yi
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jian Guan
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Huajun Xu, ; Jian Guan, ; Shankai Yin,
| | - Shankai Yin
- Department of Otolaryngology-Head and Neck Surgery and Shanghai Key Laboratory of Sleep Disordered Breathing and Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Huajun Xu, ; Jian Guan, ; Shankai Yin,
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Zhang X, Wang D, Zheng Y, Tu Y, Xu Q, Jiang H, Li C, Zhao L, Li Y, Zheng H, Gao H. Sex-dependent effects on the gut microbiota and host metabolome in type 1 diabetic mice. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166266. [PMID: 34481869 DOI: 10.1016/j.bbadis.2021.166266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 01/04/2023]
Abstract
Sexual dimorphism exists in the onset and development of type 1 diabetes (T1D), but its potential pathological mechanism is poorly understood. In the present study, we examined sex-specific changes in the gut microbiome and host metabolome of T1D mice via 16S rRNA gene sequencing and nuclear magnetic resonance (NMR)-based metabolomics approach, and aimed to investigate potential mechanism of the gut microbiota-host metabolic interaction in the sexual dimorphism of T1D. Our results demonstrate that female mice had a greater shift in the gut microbiota than male mice during the development of T1D; however, host metabolome was more susceptible to T1D in male mice. The correlation network analysis indicates that T1D-induced host metabolic changes may be regulated by the gut microbiota in a sex-specific manner, mainly involving short-chain fatty acids (SCFAs) metabolism, energy metabolism, amino acid metabolism, and choline metabolism. Therefore, our study suggests that sex-dependent "gut microbiota-host metabolism axis" may be implicated in the sexual dimorphism of T1D, and the link between microbes and metabolites might contribute to the prevention and treatment of T1D.
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Affiliation(s)
- Xi Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Die Wang
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yafei Zheng
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yingxin Tu
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qingqing Xu
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Haowei Jiang
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Chen Li
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Liangcai Zhao
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China
| | - Hong Zheng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China.
| | - Hongchang Gao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, China; Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China.
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Saiman Y, David Shen TC, Lund PJ, Gershuni VM, Jang C, Patel S, Jung S, Furth EE, Friedman ES, Chau L, Garcia BA, Wu GD. Global Microbiota-Dependent Histone Acetylation Patterns Are Irreversible and Independent of Short Chain Fatty Acids. Hepatology 2021; 74:3427-3440. [PMID: 34233020 PMCID: PMC9867598 DOI: 10.1002/hep.32043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS Although germ-free mice are an indispensable tool in studying the gut microbiome and its effects on host physiology, they are phenotypically different than their conventional counterparts. While antibiotic-mediated microbiota depletion in conventional mice leads to physiologic alterations that often mimic the germ-free state, the degree to which the effects of microbial colonization on the host are reversible is unclear. The gut microbiota produce abundant short chain fatty acids (SCFAs), and previous studies have demonstrated a link between microbial-derived SCFAs and global hepatic histone acetylation in germ-free mice. APPROACH AND RESULTS We demonstrate that global hepatic histone acetylation states measured by mass spectrometry remained largely unchanged despite loss of luminal and portal vein SCFAs after antibiotic-mediated microbiota depletion. In contrast to stable hepatic histone acetylation states, we see robust hepatic transcriptomic alterations after microbiota depletion. Additionally, neither dietary supplementation with supraphysiologic levels of SCFA nor the induction of hepatocyte proliferation in the absence of microbiota-derived SCFAs led to alterations in global hepatic histone acetylation. CONCLUSIONS These results suggest that microbiota-dependent landscaping of the hepatic epigenome through global histone acetylation is static in nature, while the hepatic transcriptome is responsive to alterations in the gut microbiota.
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Affiliation(s)
- Yedidya Saiman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ting-Chin David Shen
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peder J. Lund
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Victoria M. Gershuni
- Department of Surgery, Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Cholsoon Jang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Shivali Patel
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Emma E. Furth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau AL, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotná T, Ouattara DA, Planel S, Saliou A, Šrůtková D, Yansouni J, Stecher B, Schwarzer M, Leulier F, Tamellini A. A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes. Nat Commun 2021; 12:6686. [PMID: 34795236 PMCID: PMC8602333 DOI: 10.1038/s41467-021-26963-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.
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Affiliation(s)
- Marion Darnaud
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France.
| | - Filipe De Vadder
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Pascaline Bogeat
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Lilia Boucinha
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Anne-Laure Bulteau
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Andrei Bunescu
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Céline Couturier
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Ana Delgado
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Hélène Dugua
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Céline Elie
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Alban Mathieu
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Tereza Novotná
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | | | - Séverine Planel
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Adrien Saliou
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Dagmar Šrůtková
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | - Jennifer Yansouni
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, 54922, Nový Hrádek, Czech Republic
| | - François Leulier
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 46 Allée d'Italie, 69364, Lyon, Cedex, 07, France
| | - Andrea Tamellini
- BIOASTER, Institut de Recherche Technologique, 40 avenue Tony Garnier, 69007, Lyon, France
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Doenyas C. Potential Role of Epigenetics and Redox Signaling in the Gut-Brain Communication and the Case of Autism Spectrum Disorder. Cell Mol Neurobiol 2021; 42:483-487. [PMID: 34773541 DOI: 10.1007/s10571-021-01167-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022]
Abstract
The gut-brain axis refers to the bidirectional connection and communication between the gastrointestinal tract and the central nervous system. This paper explores two routes for this communication that have hitherto remained under-examined: epigenetics and redox signaling and their implications for autism spectrum disorder (ASD). The gut microbiota may induce epigenetic changes in the gut and potentially in the brain through their fermentation products. Instead of through other conceptualizations of them acting as neurotransmitters, gut microbial products may act as epigenetic agents, which are supported by the effects of gut bacterial-derived metabolites on gene regulation and expression. In addition to their epigenetic effects, gut bacterial-derived communicative agents can also influence host signaling by contributing to and even substituting host reactive oxygen species (ROS) production. These ROS can act as second messengers and exert oxidative activity on proteins to influence immune, inflammatory, and other signaling processes. ROS and epigenetic mechanisms may have interactive effects as well. ROS, in addition to their role in signaling pathways and cellular redox alterations, also influence redox-sensitive transcription factors, thereby having an effect on gene expression. Specifically, ROS are involved in the activation of transcription factors, chromatin remodeling, and histone/protein deacetylation. These two proposed mechanisms correspond with the recent findings related to ASD, where a cofactor that is shown to be lower in ASD has antioxidative properties, responds to epigenetic modulation, and increases via microbiota interventions. The current evidence reviewed here suggests the need to update models of the gut-brain communication to include these two mechanisms. Such a modeling can also contribute to understanding the unknowns of host metabolism and physiology in ASD and afford potential therapeutic avenues for this as well as other psychiatric and physiological conditions.
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81
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Zhang W, An Y, Qin X, Wu X, Wang X, Hou H, Song X, Liu T, Wang B, Huang X, Cao H. Gut Microbiota-Derived Metabolites in Colorectal Cancer: The Bad and the Challenges. Front Oncol 2021; 11:739648. [PMID: 34733783 PMCID: PMC8558397 DOI: 10.3389/fonc.2021.739648] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence from studies in humans and animal models has elucidated that gut microbiota, acting as a complex ecosystem, contributes critically to colorectal cancer (CRC). The potential mechanisms often reported emphasize the vital role of carcinogenic activities of specific pathogens, but in fact, a series of metabolites produced from exogenous dietary substrates or endogenous host compounds occupy a decisive position similarly. Detrimental gut microbiota-derived metabolites such as trimethylamine-N-oxide, secondary bile acids, hydrogen sulfide and N-nitroso compounds could reconstruct the ecological composition and metabolic activity of intestinal microorganisms and formulate a microenvironment that opens susceptibility to carcinogenic stimuli. They are implicated in the occurrence, progression and metastasis of CRC through different mechanisms, including inducing inflammation and DNA damage, activating tumorigenic signaling pathways and regulating tumor immunity. In this review, we mainly summarized the intimate relationship between detrimental gut microbiota-derived metabolites and CRC, and updated the current knowledge about detrimental metabolites in CRC pathogenesis. Then, multiple interventions targeting these metabolites for CRC management were critically reviewed, including diet modulation, probiotics/prebiotics, fecal microbiota transplantation, as well as more precise measures such as engineered bacteria, phage therapy and chemopreventive drugs. A better understanding of the interplay between detrimental microbial metabolites and CRC would hold great promise against CRC.
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Affiliation(s)
- Wanru Zhang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yaping An
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xuemei Wu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xinyu Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Huiqin Hou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xueli Song
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xuan Huang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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82
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Santoro A, Bientinesi E, Monti D. Immunosenescence and inflammaging in the aging process: age-related diseases or longevity? Ageing Res Rev 2021; 71:101422. [PMID: 34391943 DOI: 10.1016/j.arr.2021.101422] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
During aging the immune system (IS) undergoes remarkable changes that collectively are known as immunosenescence. It is a multifactorial and dynamic phenomenon that affects both natural and acquired immunity and plays a critical role in most chronic diseases in older people. For a long time, immunosenescence has been considered detrimental because it may lead to a low-grade, sterile chronic inflammation we proposed to call "inflammaging" and a progressive reduction in the ability to trigger effective antibody and cellular responses against infections and vaccinations. Recently, many scientists revised this negative meaning because it can be considered an essential adaptation/remodeling resulting from the lifelong immunological biography of single individuals from an evolutionary perspective. Inflammaging can be considered an adaptive process because it can trigger an anti-inflammatory response to counteract the age-related pro-inflammatory environment. Centenarians represent a valuable model to study the beneficial changes occurring in the IS with age. These extraordinary individuals reached the extreme limits of human life by slowing down the aging process and, in most cases, delaying, avoiding or surviving the major age-associated diseases. They indeed show a complex and heterogeneous phenotype determined by an improved ability to adapt and remodel in response to harmful stimuli. This review aims to point out the intimate relationship between immunosenescence and inflammaging and how these processes impact unsuccessful aging rather than longevity. We also describe the gut microbiota age-related changes as one of the significant triggers of inflammaging and the sex/gender differences in the immune system of the elderly, contributing to the sex/gender disparity in terms of epidemiology, pathophysiology, symptoms and severity of age-related diseases. Finally, we discuss how these phenomena could influence the susceptibility to COVID-19 infection.
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83
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Prokopidis K, Chambers E, Ni Lochlainn M, Witard OC. Mechanisms Linking the Gut-Muscle Axis With Muscle Protein Metabolism and Anabolic Resistance: Implications for Older Adults at Risk of Sarcopenia. Front Physiol 2021; 12:770455. [PMID: 34764887 PMCID: PMC8576575 DOI: 10.3389/fphys.2021.770455] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is associated with a decline in skeletal muscle mass and function-termed sarcopenia-as mediated, in part, by muscle anabolic resistance. This metabolic phenomenon describes the impaired response of muscle protein synthesis (MPS) to the provision of dietary amino acids and practice of resistance-based exercise. Recent observations highlight the gut-muscle axis as a physiological target for combatting anabolic resistance and reducing risk of sarcopenia. Experimental studies, primarily conducted in animal models of aging, suggest a mechanistic link between the gut microbiota and muscle atrophy, mediated via the modulation of systemic amino acid availability and low-grade inflammation that are both physiological factors known to underpin anabolic resistance. Moreover, in vivo and in vitro studies demonstrate the action of specific gut bacteria (Lactobacillus and Bifidobacterium) to increase systemic amino acid availability and elicit an anti-inflammatory response in the intestinal lumen. Prospective lifestyle approaches that target the gut-muscle axis have recently been examined in the context of mitigating sarcopenia risk. These approaches include increasing dietary fiber intake that promotes the growth and development of gut bacteria, thus enhancing the production of short-chain fatty acids (SCFA) (acetate, propionate, and butyrate). Prebiotic/probiotic/symbiotic supplementation also generates SCFA and may mitigate low-grade inflammation in older adults via modulation of the gut microbiota. Preliminary evidence also highlights the role of exercise in increasing the production of SCFA. Accordingly, lifestyle approaches that combine diets rich in fiber and probiotic supplementation with exercise training may serve to produce SCFA and increase microbial diversity, and thus may target the gut-muscle axis in mitigating anabolic resistance in older adults. Future mechanistic studies are warranted to establish the direct physiological action of distinct gut microbiota phenotypes on amino acid utilization and the postprandial stimulation of muscle protein synthesis in older adults.
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Affiliation(s)
- Konstantinos Prokopidis
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Edward Chambers
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Mary Ni Lochlainn
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Oliver C. Witard
- Faculty of Life Sciences and Medicine, Centre for Human and Applied Physiological Sciences, King’s College London, London, United Kingdom
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84
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Altered microbiota-host metabolic cross talk preceding neutropenic fever in patients with acute leukemia. Blood Adv 2021; 5:3937-3950. [PMID: 34478486 PMCID: PMC8945620 DOI: 10.1182/bloodadvances.2021004973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/03/2021] [Indexed: 01/09/2023] Open
Abstract
In 2 cohorts of patients with acute leukemia, Akkermansia expansion in the gut predicted a higher risk for neutropenic fever. Metabolomics analysis suggested oxidative stress as the mediating pathway, thus offering potential targets for personalized prophylaxis.
Despite antibiotic prophylaxis, most patients with acute leukemia receiving mucotoxic chemotherapy develop neutropenic fever (NF), many cases of which remain without a documented etiology. Antibiotics disrupt the gut microbiota, with adverse clinical consequences, such as Clostridioides difficile infection. A better understanding of NF pathogenesis could inform the development of novel therapeutics without deleterious effects on the microbiota. We hypothesized that metabolites absorbed from the gut to the bloodstream modulate pyrogenic and inflammatory pathways. Longitudinal profiling of the gut microbiota in 2 cohorts of patients with acute leukemia showed that Akkermansia expansion in the gut was associated with an increased risk for NF. As a prototype mucolytic genus, Akkermansia may influence the absorption of luminal metabolites; thus, its association with NF supported our metabolomics hypothesis. Longitudinal profiling of the serum metabolome identified a signature associated with gut Akkermansia and 1 with NF. Importantly, these 2 signatures overlapped in metabolites in the γ-glutamyl cycle, suggesting oxidative stress as a mediator involved in Akkermansia-related NF. In addition, the level of gut microbial–derived indole compounds increased after Akkermansia expansion and decreased before NF, suggesting their role in mediating the anti-inflammatory effects of Akkermansia, as seen predominantly in healthy individuals. These results suggest that Akkermansia regulates microbiota-host metabolic cross talk by modulating the mucosal interface. The clinical context, including factors influencing microbiota composition, determines the type of metabolites absorbed through the gut barrier and their net effect on the host. Our findings identify novel aspects of NF pathogenesis that could be targets for precision therapeutics. This trial was registered at www.clinicaltrials.gov as #NCT03316456.
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85
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Yang H, Mayneris-Perxachs J, Boqué N, del Bas JM, Arola L, Yuan M, Türkez H, Uhlén M, Borén J, Zhang C, Mardinoglu A, Caimari A. Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet. Biomedicines 2021; 9:1440. [PMID: 34680557 PMCID: PMC8533474 DOI: 10.3390/biomedicines9101440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/13/2023] Open
Abstract
Although the prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase, there is no effective treatment approved for this condition. We previously showed, in high-fat diet (HFD)-fed mice, that the supplementation of combined metabolic activators (CMA), including nicotinamide riboside (NAD+ precursor) and the potent glutathione precursors serine and N-acetyl-l-cysteine (NAC), significantly decreased fatty liver by promoting fat oxidation in mitochondria. Afterwards, in a one-day proof-of-concept human supplementation study, we observed that this CMA, including also L-carnitine tartrate (LCT), resulted in increased fatty acid oxidation and de novo glutathione synthesis. However, the underlying molecular mechanisms associated with supplementation of CMA have not been fully elucidated. Here, we demonstrated in hamsters that the chronic supplementation of this CMA (changing serine for betaine) at two doses significantly decreased hepatic steatosis. We further generated liver transcriptomics data and integrated these data using a liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMA and found that it activates mitochondria in the liver tissue by modulating global lipid, amino acid, antioxidant and folate metabolism. Our findings provide extra evidence about the beneficial effects of a treatment based on this CMA against NAFLD.
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Affiliation(s)
- Hong Yang
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Girona Biomedical Research Institute (IDIBGI), Hospital Universitari de Girona Doctor Josep Trueta, 17190 Girona, Spain;
- Center for Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Noemí Boqué
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
| | - Josep M. del Bas
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
| | - Lluís Arola
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
- Nutrigenomics Research Group, Department of Biochemistry and Biotechnology, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Meng Yuan
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Hasan Türkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25030, Turkey;
| | - Mathias Uhlén
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, SE-40233 Gothenburg, Sweden;
| | - Cheng Zhang
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden; (H.Y.); (M.Y.); (M.U.); (C.Z.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London WC2R 2LS, UK
| | - Antoni Caimari
- Eurecat, Centre Tecnològic de Catalunya, Technological Unit of Nutrition and Health, 43204 Reus, Spain; (N.B.); (J.M.d.B.); (L.A.)
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86
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Ezzamouri B, Shoaie S, Ledesma-Amaro R. Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies. Front Microbiol 2021; 12:681982. [PMID: 34531833 PMCID: PMC8438329 DOI: 10.3389/fmicb.2021.681982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.
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Affiliation(s)
- Bouchra Ezzamouri
- Unit for Population-Based Dermatology Research, St John’s Institute of Dermatology, Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kindom
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Saeed Shoaie
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
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87
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Wang H, Robinson JL, Kocabas P, Gustafsson J, Anton M, Cholley PE, Huang S, Gobom J, Svensson T, Uhlen M, Zetterberg H, Nielsen J. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proc Natl Acad Sci U S A 2021; 118:e2102344118. [PMID: 34282017 PMCID: PMC8325244 DOI: 10.1073/pnas.2102344118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and metabolic malfunctions. However, the lack of comprehensive and high-quality GEMs for model organisms restricts translational utilization of omics data accumulating from the use of various disease models. Here we present a unified platform of GEMs that covers five major model animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), and Worm1 (Caenorhabditis elegans). These GEMs represent the most comprehensive coverage of the metabolic network by considering both orthology-based pathways and species-specific reactions. All GEMs can be interactively queried via the accompanying web portal Metabolic Atlas. Specifically, through integrative analysis of Mouse1 with RNA-sequencing data from brain tissues of transgenic mice we identified a coordinated up-regulation of lysosomal GM2 ganglioside and peptide degradation pathways which appears to be a signature metabolic alteration in Alzheimer's disease (AD) mouse models with a phenotype of amyloid precursor protein overexpression. This metabolic shift was further validated with proteomics data from transgenic mice and cerebrospinal fluid samples from human patients. The elevated lysosomal enzymes thus hold potential to be used as a biomarker for early diagnosis of AD. Taken together, we foresee that this evolving open-source platform will serve as an important resource to facilitate the development of systems medicines and translational biomedical applications.
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Affiliation(s)
- Hao Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jonathan L Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Pinar Kocabas
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Johan Gustafsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Mihail Anton
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Pierre-Etienne Cholley
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Shan Huang
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, 431 30 Mölndal, Sweden
| | - Thomas Svensson
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Mattias Uhlen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Wallenberg Center for Protein Research, KTH-Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, 431 30 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 30 Mölndal, Sweden
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London WC1E 6BT, United Kingdom
- UK Dementia Research Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden;
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- BioInnovation Institute, DK2200 Copenhagen, Denmark
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88
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Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of D-Galactose-Induced Aging Rats Fed with High-Fat Diet. Probiotics Antimicrob Proteins 2021; 12:545-562. [PMID: 31301059 DOI: 10.1007/s12602-019-09545-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Both aging and diet play an important role in influencing the gut ecosystem. Using premature senescent rats induced by D-galactose and fed with high-fat diet, this study aims to investigate the effects of different potential probiotic strains on the dynamic changes of fecal microbiome and metabolites. In this study, male Sprague-Dawley rats were fed with high-fat diet and injected with D-galactose for 12 weeks to induce aging. The effect of Lactobacillus plantarum DR7, L. fermentum DR9, and L. reuteri 8513d administration on the fecal microbiota profile, short-chain fatty acids, and water-soluble compounds were analyzed. It was found that the administration of the selected strains altered the gut microbiota diversity and composition, even at the phylum level. The fecal short-chain fatty acid content was also higher in groups that were administered with the potential probiotic strains. Analysis of the fecal water-soluble metabolites revealed that administration of L. plantarum DR7 and L. reuteri 8513d led to higher fecal content of compounds related to amino acid metabolism such as tryptophan, leucine, tyrosine, cysteine, methionine, valine, and lysine; while administration of L. fermentum DR9 led to higher prevalence of compounds related to carbohydrate metabolism such as erythritol, xylitol, and arabitol. In conclusion, it was observed that different strains of lactobacilli can cause difference alteration in the gut microbiota and the metabolites, suggesting the urgency to explore the specific metabolic impact of specific strains on the host.
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89
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Conway J, A Duggal N. Ageing of the gut microbiome: Potential influences on immune senescence and inflammageing. Ageing Res Rev 2021; 68:101323. [PMID: 33771720 DOI: 10.1016/j.arr.2021.101323] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 02/08/2023]
Abstract
Advancing age is accompanied by changes in the gut microbiota characterised by a loss of beneficial commensal microbes that is driven by intrinsic and extrinsic factors such as diet, medications, sedentary behaviour and chronic health conditions. Concurrently, ageing is accompanied by an impaired ability to mount a robust immune response, termed immunesenescence, and age-associated inflammation, termed inflammaging. The microbiome has been proposed to impact the immune system and is a potential determinant of healthy aging. In this review we summarise the knowledge on the impact of ageing on microbial dysbiosis, intestinal permeability, inflammaging, and the immune system and investigate whether dysbiosis of the gut microbiota could be a potential mechanism underlying the decline in immune function, overall health and longevity with advancing age. Furthermore, we examine the potential of altering the gut microbiome composition as a novel intervention strategy to reverse the immune ageing clock and possibly support overall good health during old age.
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90
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Chen LM, Bao CH, Wu Y, Liang SH, Wang D, Wu LY, Huang Y, Liu HR, Wu HG. Tryptophan-kynurenine metabolism: a link between the gut and brain for depression in inflammatory bowel disease. J Neuroinflammation 2021; 18:135. [PMID: 34127024 PMCID: PMC8204445 DOI: 10.1186/s12974-021-02175-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/13/2021] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD), which mainly includes ulcerative colitis (UC) and Crohn's disease (CD), is a group of chronic bowel diseases that are characterized by abdominal pain, diarrhea, and bloody stools. IBD is strongly associated with depression, and its patients have a higher incidence of depression than the general population. Depression also adversely affects the quality of life and disease prognosis of patients with IBD. The tryptophan-kynurenine metabolic pathway degrades more than 90% of tryptophan (TRP) throughout the body, with indoleamine 2,3-dioxygenase (IDO), the key metabolic enzyme, being activated in the inflammatory environment. A series of metabolites of the pathway are neurologically active, among which kynerunic acid (KYNA) and quinolinic acid (QUIN) are molecules of great interest in recent studies on the mechanisms of inflammation-induced depression. In this review, the relationship between depression in IBD and the tryptophan-kynurenine metabolic pathway is overviewed in the light of recent publications.
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Affiliation(s)
- Li-Ming Chen
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China
| | - Chun-Hui Bao
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China.
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China.
| | - Yu Wu
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China
| | - Shi-Hua Liang
- Faculty of Economics and Business, University of Groningen, Nettelbosje 2, Groningen, 9747 AE, The Netherlands
| | - Di Wang
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China
| | - Lu-Yi Wu
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China
| | - Yan Huang
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China
| | - Hui-Rong Liu
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China
| | - Huan-Gan Wu
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110 Ganhe Road, Shanghai, 200437, China.
- Key Laboratory of Acupuncture and Immunological Effects, Shanghai University of Traditional Chinese Medicine, No. 650 South Wanping Road, Shanghai, 200030, China.
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91
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Haque M, Koski KG, Scott ME. A gastrointestinal nematode in pregnant and lactating mice alters maternal and neonatal microbiomes. Int J Parasitol 2021; 51:945-957. [PMID: 34081970 DOI: 10.1016/j.ijpara.2021.03.008] [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: 08/19/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/29/2022]
Abstract
The maternal microbiome is understood to be the principal source of the neonatal microbiome but the consequences of intestinal nematodes on pregnant and lactating mothers and implications for the neonatal microbiome are unknown. Using pregnant CD1 mice infected with Heligmosomoides bakeri, we investigated the microbiomes in maternal tissues (intestine, vagina, and milk) and in the neonatal stomach using MiSeq sequencing of bacterial 16S rRNA genes. Our first hypothesis was that maternal nematode infection altered the maternal intestinal, vaginal, and milk microbiomes and associated metabolic pathways. Maternal nematode infection was associated with increased beta-diversity and abundance of fermenting bacteria as well as Lactobacillus in the maternal caecum 2 days after parturition, together with down-regulated carbohydrate, amino acid and vitamin biosynthesis pathways. Maternal nematode infection did not alter the vaginal or milk microbiomes. Our second hypothesis was that maternal infection would shape colonization of the neonatal microbiome. Although the pup stomach microbiome was similar to that of the maternal vaginal microbiome, pups of infected dams had higher beta-diversity at day 2, and a dramatic expansion in the abundance of Lactobacillus between days 2 and 7 compared with pups nursing uninfected dams. Our third hypothesis that maternal nematode infection altered the composition of neonatal microbiomes was confirmed as we observed up-regulation of several putatively beneficial microbial pathways associated with synthesis of essential and branched-chain amino acids, vitamins, and short-chain fatty acids. We believe this is the first study to show that a nematode living in the maternal intestine is associated with altered composition and function of the neonatal microbiome.
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Affiliation(s)
- Manjurul Haque
- Institute of Parasitology, McGill University (Macdonald Campus), 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Kristine G Koski
- School of Human Nutrition, McGill University (Macdonald Campus), 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Marilyn E Scott
- Institute of Parasitology, McGill University (Macdonald Campus), 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada.
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92
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Hoozemans J, de Brauw M, Nieuwdorp M, Gerdes V. Gut Microbiome and Metabolites in Patients with NAFLD and after Bariatric Surgery: A Comprehensive Review. Metabolites 2021; 11:353. [PMID: 34072995 PMCID: PMC8227414 DOI: 10.3390/metabo11060353] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing, as are other manifestations of metabolic syndrome such as obesity and type 2 diabetes. NAFLD is currently the number one cause of chronic liver disease worldwide. The pathophysiology of NAFLD and disease progression is poorly understood. A potential contributing role for gut microbiome and metabolites in NAFLD is proposed. Currently, bariatric surgery is an effective therapy to prevent the progression of NAFLD and other manifestations of metabolic syndrome such as obesity and type 2 diabetes. This review provides an overview of gut microbiome composition and related metabolites in individuals with NAFLD and after bariatric surgery. Causality remains to be proven. Furthermore, the clinical effects of bariatric surgery on NAFLD are illustrated. Whether the gut microbiome and metabolites contribute to the metabolic improvement and improvement of NAFLD seen after bariatric surgery has not yet been proven. Future microbiome and metabolome research is necessary for elucidating the pathophysiology and underlying metabolic pathways and phenotypes and providing better methods for diagnostics, prognostics and surveillance to optimize clinical care.
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Affiliation(s)
- Jacqueline Hoozemans
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, AMC, 1105 AZ Amsterdam, The Netherlands; (M.N.); (V.G.)
- Department of Bariatric and General Surgery, Spaarne Hospital, 2134 TM Hoofddorp, The Netherlands;
| | - Maurits de Brauw
- Department of Bariatric and General Surgery, Spaarne Hospital, 2134 TM Hoofddorp, The Netherlands;
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, AMC, 1105 AZ Amsterdam, The Netherlands; (M.N.); (V.G.)
| | - Victor Gerdes
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, AMC, 1105 AZ Amsterdam, The Netherlands; (M.N.); (V.G.)
- Department of Internal Medicine, Spaarne Hospital, 2134 TM Hoofddorp, The Netherlands
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93
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Abdallah A, Elemba E, Zhong Q, Sun Z. Gastrointestinal Interaction between Dietary Amino Acids and Gut Microbiota: With Special Emphasis on Host Nutrition. Curr Protein Pept Sci 2021; 21:785-798. [PMID: 32048965 DOI: 10.2174/1389203721666200212095503] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022]
Abstract
The gastrointestinal tract (GIT) of humans and animals is host to a complex community of different microorganisms whose activities significantly influence host nutrition and health through enhanced metabolic capabilities, protection against pathogens, and regulation of the gastrointestinal development and immune system. New molecular technologies and concepts have revealed distinct interactions between the gut microbiota and dietary amino acids (AAs) especially in relation to AA metabolism and utilization in resident bacteria in the digestive tract, and these interactions may play significant roles in host nutrition and health as well as the efficiency of dietary AA supplementation. After the protein is digested and AAs and peptides are absorbed in the small intestine, significant levels of endogenous and exogenous nitrogenous compounds enter the large intestine through the ileocaecal junction. Once they move in the colonic lumen, these compounds are not markedly absorbed by the large intestinal mucosa, but undergo intense proteolysis by colonic microbiota leading to the release of peptides and AAs and result in the production of numerous bacterial metabolites such as ammonia, amines, short-chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs), hydrogen sulfide, organic acids, and phenols. These metabolites influence various signaling pathways in epithelial cells, regulate the mucosal immune system in the host, and modulate gene expression of bacteria which results in the synthesis of enzymes associated with AA metabolism. This review aims to summarize the current literature relating to how the interactions between dietary amino acids and gut microbiota may promote host nutrition and health.
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Affiliation(s)
- Abedin Abdallah
- Key laboratory of Straw Biology and Utilization (The Ministry of Education), Key Lab of Animal Nutrition and Feed
Science, Key Lab of Animal Production, Product Quality and Security, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Evera Elemba
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Qingzhen Zhong
- Key laboratory of Straw Biology and Utilization (The Ministry of Education), Key Lab of Animal Nutrition and Feed
Science, Key Lab of Animal Production, Product Quality and Security, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zewei Sun
- Key laboratory of Straw Biology and Utilization (The Ministry of Education), Key Lab of Animal Nutrition and Feed
Science, Key Lab of Animal Production, Product Quality and Security, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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94
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Jiang PP, Muk T, Krych L, Nielsen DS, Khakimov B, Li Y, Juhl SM, Greisen G, Sangild PT. Gut colonization in preterm infants supplemented with bovine colostrum in the first week of life: An explorative pilot study. JPEN J Parenter Enteral Nutr 2021; 46:592-599. [PMID: 33988859 DOI: 10.1002/jpen.2191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND In the first weeks after birth, enteral feeding and bacterial colonization interact to influence gut maturation in preterm infants. Bovine colostrum (BC) has been suggested as a relevant supplementary diet when own mother's milk (MM) is insufficient or absent. This pilot trial tests whether the supplement type, BC or donor human milk (DM), affects gut colonization in preterm infants during the first week of life. METHODS On day 7, fecal samples were collected from preterm infants (n = 24) fed BC or DM as a supplement to MM. The gut microbiome (GM) was analyzed by 16S ribosomal RNA amplicon sequencing. Correlations between the relative abundance of specific bacterial taxa and blood chemistry variables, including amino acids, were explored. RESULTS BC-supplemented infants showed a lower relative abundance of the families Lactobacillaceae and Enterococcaceae than DM infants. Planococcaceae were more abundant in infants delivered by cesarean birth vs vaginally. The relative abundance of bacterial families, specifically Enterobacteriaceae, correlated negatively with plasma levels of multiple essential and nonessential amino acids (valine, isoleucine, lysine, histidine, and arginine). CONCLUSION The nature of nutrition supplements (BC or DM) just after birth may affect GM development and nutrient metabolism in the neonatal period of preterm infants. The exploratory nature of our study calls for confirmation of these results and their possible long-term clinical implications for preterm infants.
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Affiliation(s)
- Ping-Ping Jiang
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China.,Comparative Paediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tik Muk
- Comparative Paediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Yanqi Li
- Comparative Paediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Gorm Greisen
- Department of Neonatology, Rigshospitalet, Copenhagen, Denmark
| | - Per Torp Sangild
- Comparative Paediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Neonatology, Rigshospitalet, Copenhagen, Denmark.,Department of Paediatrics, Odense University Hospital, Odense, Denmark
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95
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Arif M, Klevstig M, Benfeitas R, Doran S, Turkez H, Uhlén M, Clausen M, Wikström J, Etal D, Zhang C, Levin M, Mardinoglu A, Boren J. Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction. eLife 2021; 10:66921. [PMID: 33972017 PMCID: PMC8186902 DOI: 10.7554/elife.66921] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Myocardial infarction (MI) promotes a range of systemic effects, many of which are unknown. Here, we investigated the alterations associated with MI progression in heart and other metabolically active tissues (liver, skeletal muscle, and adipose) in a mouse model of MI (induced by ligating the left ascending coronary artery) and sham-operated mice. We performed a genome-wide transcriptomic analysis on tissue samples obtained 6- and 24 hr post MI or sham operation. By generating tissue-specific biological networks, we observed: (1) dysregulation in multiple biological processes (including immune system, mitochondrial dysfunction, fatty-acid beta-oxidation, and RNA and protein processing) across multiple tissues post MI and (2) tissue-specific dysregulation in biological processes in liver and heart post MI. Finally, we validated our findings in two independent MI cohorts. Overall, our integrative analysis highlighted both common and specific biological responses to MI across a range of metabolically active tissues. The human body is like a state-of-the-art car, where each part must work together with all the others. When a car breaks down, most of the time the problem is not isolated to only one part, as it is an interconnected system. Diseases in the human body can also have systemic effects, so it is important to study their implications throughout the body. Most studies of heart attacks focus on the direct impact on the heart and the cardiovascular system. Learning more about how heart attacks affect rest of the body may help scientists identify heart attacks early or create improved treatments. Arif and Klevstig et al. show that heart attacks affect the metabolism throughout the body. In the experiments, mice underwent a procedure that mimics either a heart attack or a fake procedure. Then, Arif and Klevstig et al. compared the activity of genes in the heart, muscle, liver and fat tissue of the two groups of mice 6- and 24-hours after the operations. This revealed disruptions in the immune system, metabolism and the production of proteins. The experiments also showed that changes in the activity of four important genes are key to these changes. This suggests that this pattern of changes could be used as a way to identify heart attacks. The experiments show that heart attacks have important effects throughout the body, especially on metabolism. These discoveries may help scientists learn more about the underlying biological processes and develop new treatments that prevent the harmful systemic effects of heart attacks and boost recovery.
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Affiliation(s)
- Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martina Klevstig
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Stephen Doran
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Maryam Clausen
- Translational Genomics, BioPharmaceuticals R&D, Discovery Sciences, AstraZeneca, Gothenburg, Sweden
| | - Johannes Wikström
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Damla Etal
- Translational Genomics, BioPharmaceuticals R&D, Discovery Sciences, AstraZeneca, Gothenburg, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Malin Levin
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
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96
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Barretto SA, Lasserre F, Huillet M, Régnier M, Polizzi A, Lippi Y, Fougerat A, Person E, Bruel S, Bétoulières C, Naylies C, Lukowicz C, Smati S, Guzylack L, Olier M, Théodorou V, Mselli-Lakhal L, Zalko D, Wahli W, Loiseau N, Gamet-Payrastre L, Guillou H, Ellero-Simatos S. The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice. MICROBIOME 2021; 9:93. [PMID: 33879258 PMCID: PMC8059225 DOI: 10.1186/s40168-021-01050-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/16/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The gut microbiota-intestine-liver relationship is emerging as an important factor in multiple hepatic pathologies, but the hepatic sensors and effectors of microbial signals are not well defined. RESULTS By comparing publicly available liver transcriptomics data from conventional vs. germ-free mice, we identified pregnane X receptor (PXR, NR1I2) transcriptional activity as strongly affected by the absence of gut microbes. Microbiota depletion using antibiotics in Pxr+/+ vs Pxr-/- C57BL/6J littermate mice followed by hepatic transcriptomics revealed that most microbiota-sensitive genes were PXR-dependent in the liver in males, but not in females. Pathway enrichment analysis suggested that microbiota-PXR interaction controlled fatty acid and xenobiotic metabolism. We confirmed that antibiotic treatment reduced liver triglyceride content and hampered xenobiotic metabolism in the liver from Pxr+/+ but not Pxr-/- male mice. CONCLUSIONS These findings identify PXR as a hepatic effector of microbiota-derived signals that regulate the host's sexually dimorphic lipid and xenobiotic metabolisms in the liver. Thus, our results reveal a potential new mechanism for unexpected drug-drug or food-drug interactions. Video abstract.
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Affiliation(s)
- Sharon Ann Barretto
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Frederic Lasserre
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Marine Huillet
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Marion Régnier
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Arnaud Polizzi
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Yannick Lippi
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Anne Fougerat
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Elodie Person
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Sandrine Bruel
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Colette Bétoulières
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Claire Naylies
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Céline Lukowicz
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Sarra Smati
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Laurence Guzylack
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Maïwenn Olier
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Vassilia Théodorou
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Laila Mselli-Lakhal
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Daniel Zalko
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Walter Wahli
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore
- Center for Integrative Genomics, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Nicolas Loiseau
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Laurence Gamet-Payrastre
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Hervé Guillou
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Sandrine Ellero-Simatos
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France.
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Sipos A, Ujlaki G, Mikó E, Maka E, Szabó J, Uray K, Krasznai Z, Bai P. The role of the microbiome in ovarian cancer: mechanistic insights into oncobiosis and to bacterial metabolite signaling. Mol Med 2021; 27:33. [PMID: 33794773 PMCID: PMC8017782 DOI: 10.1186/s10020-021-00295-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancer is characterized by dysbiosis, referred to as oncobiosis in neoplastic diseases. In ovarian cancer, oncobiosis was identified in numerous compartments, including the tumor tissue itself, the upper and lower female genital tract, serum, peritoneum, and the intestines. Colonization was linked to Gram-negative bacteria with high inflammatory potential. Local inflammation probably participates in the initiation and continuation of carcinogenesis. Furthermore, local bacterial colonies in the peritoneum may facilitate metastasis formation in ovarian cancer. Vaginal infections (e.g. Neisseria gonorrhoeae or Chlamydia trachomatis) increase the risk of developing ovarian cancer. Bacterial metabolites, produced by the healthy eubiome or the oncobiome, may exert autocrine, paracrine, and hormone-like effects, as was evidenced in breast cancer or pancreas adenocarcinoma. We discuss the possible involvement of lipopolysaccharides, lysophosphatides and tryptophan metabolites, as well as, short-chain fatty acids, secondary bile acids and polyamines in the carcinogenesis of ovarian cancer. We discuss the applicability of nutrients, antibiotics, and probiotics to harness the microbiome and support ovarian cancer therapy. The oncobiome and the most likely bacterial metabolites play vital roles in mediating the effectiveness of chemotherapy. Finally, we discuss the potential of oncobiotic changes as biomarkers for the diagnosis of ovarian cancer and microbial metabolites as possible adjuvant agents in therapy.
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Affiliation(s)
- Adrienn Sipos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Gyula Ujlaki
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Edit Mikó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Eszter Maka
- Department of Gynecology and Obstetrics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Judit Szabó
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Zoárd Krasznai
- Department of Gynecology and Obstetrics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary.
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, 4032, Hungary.
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary.
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98
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Chi X, Liu Z, Wang H, Wang Y, Wei W, Xu B. Royal jelly enhanced the antioxidant activities and modulated the gut microbiota in healthy mice. J Food Biochem 2021; 45:e13701. [PMID: 33792081 DOI: 10.1111/jfbc.13701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 12/16/2022]
Abstract
Royal jelly (RJ) is a well-known traditional health food that has a wide range of pharmacological activities. In this study, mice were fed with different doses of RJ for 30 days and their antioxidant activities and gut microbiota were measured to examine the correlation between gut microbiota and overall health. RJ did not influence the feed consumption or relative organ weight, but RJ did increase the amount of serum interleukin 10 (IL-10), as well as the levels of antioxidant activities in the liver and kidney. The middle dose of RJ (RJM) decreased the relative abundance of Proteobacteria at phylum level, increased the relative abundance of Lachnospiraceae_NK4A136_group and Bacteroides. Correlation analysis indicated that RJ could optimize the functional network of gut microbiota and the interactions between the gut microbiota and the host. In conclusion, RJ could enhance the antioxidant activities and modulate the gut microbiota. RJM treatment had a more positive effect on physical health compared with RJL and RJH treatments. PRACTICAL APPLICATIONS: Royal jelly is a healthy dietary supplement which has a wide range of functions. The research helps us know the action mechanism of RJ in healthy body and analyzed the correlation of gut microbiota and physiological state. The appropriate dose of RJ was also studied and the health functions of RJ for healthy body were proved. This research could help to increase the RJ consuming in market.
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Affiliation(s)
- Xuepeng Chi
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Wei Wei
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
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99
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Firmino JP, Vallejos-Vidal E, Balebona MC, Ramayo-Caldas Y, Cerezo IM, Salomón R, Tort L, Estevez A, Moriñigo MÁ, Reyes-López FE, Gisbert E. Diet, Immunity, and Microbiota Interactions: An Integrative Analysis of the Intestine Transcriptional Response and Microbiota Modulation in Gilthead Seabream ( Sparus aurata) Fed an Essential Oils-Based Functional Diet. Front Immunol 2021; 12:625297. [PMID: 33746962 PMCID: PMC7969985 DOI: 10.3389/fimmu.2021.625297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Essential oils (EOs) are promising alternatives to chemotherapeutics in animal production due to their immunostimulant, antimicrobial, and antioxidant properties, without associated environmental or hazardous side effects. In the present study, the modulation of the transcriptional immune response (microarray analysis) and microbiota [16S Ribosomal RNA (rRNA) sequencing] in the intestine of the euryhaline fish gilthead seabream (Sparus aurata) fed a dietary supplementation of garlic, carvacrol, and thymol EOs was evaluated. The transcriptomic functional analysis showed the regulation of genes related to processes of proteolysis and inflammatory modulation, immunity, transport and secretion, response to cyclic compounds, symbiosis, and RNA metabolism in fish fed the EOs-supplemented diet. Particularly, the activation of leukocytes, such as acidophilic granulocytes, was suggested to be the primary actors of the innate immune response promoted by the tested functional feed additive in the gut. Fish growth performance and gut microbiota alpha diversity indices were not affected, while dietary EOs promoted alterations in bacterial abundances in terms of phylum, class, and genus. Subtle, but significant alterations in microbiota composition, such as the decrease in Bacteroidia and Clostridia classes, were suggested to participate in the modulation of the intestine transcriptional immune profile observed in fish fed the EOs diet. Moreover, regarding microbiota functionality, increased bacterial sequences associated with glutathione and lipid metabolisms, among others, detected in fish fed the EOs supported the metabolic alterations suggested to potentially affect the observed immune-related transcriptional response. The overall results indicated that the tested dietary EOs may promote intestinal local immunity through the impact of the EOs on the host-microbial co-metabolism and consequent regulation of significant biological processes, evidencing the crosstalk between gut and microbiota in the inflammatory regulation upon administration of immunostimulant feed additives.
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Affiliation(s)
- Joana P. Firmino
- IRTA, Centre de Sant Carles de la Ràpita (IRTA-SCR), Aquaculture Program, Sant Carles de la Ràpita, Spain
- TECNOVIT–FARMFAES, S.L. Alforja, Spain
- Ph.D. Program in Aquaculture, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eva Vallejos-Vidal
- Departamento de Biología, Facultad de Química y Biología, Centro de Biotecnología Acuícola, Universidad de Santiago de Chile, Santiago, Chile
| | - M. Carmen Balebona
- Department of Microbiology, Faculty of Science, University of Malaga, Málaga, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Torre Marimon, Caldes de Montbui, Spain
| | - Isabel M. Cerezo
- Department of Microbiology, Faculty of Science, University of Malaga, Málaga, Spain
| | - Ricardo Salomón
- IRTA, Centre de Sant Carles de la Ràpita (IRTA-SCR), Aquaculture Program, Sant Carles de la Ràpita, Spain
- Ph.D. Program in Aquaculture, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lluis Tort
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alicia Estevez
- IRTA, Centre de Sant Carles de la Ràpita (IRTA-SCR), Aquaculture Program, Sant Carles de la Ràpita, Spain
| | | | - Felipe E. Reyes-López
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
- Consorcio Tecnológico de Sanidad Acuícola, Ictio Biotechnologies S. A., Santiago, Chile
| | - Enric Gisbert
- IRTA, Centre de Sant Carles de la Ràpita (IRTA-SCR), Aquaculture Program, Sant Carles de la Ràpita, Spain
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100
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Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A, Shoaie S. Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease. Cell Rep 2021; 34:108807. [PMID: 33657381 DOI: 10.1016/j.celrep.2021.108807] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/22/2020] [Accepted: 02/09/2021] [Indexed: 01/06/2023] Open
Abstract
Parkinson's disease (PD) is the most common progressive neurological disorder compromising motor functions. However, nonmotor symptoms, such as gastrointestinal (GI) dysfunction, precede those affecting movement. Evidence of an early involvement of the GI tract and enteric nervous system highlights the need for better understanding of the role of gut microbiota in GI complications in PD. Here, we investigate the gut microbiome of patients with PD using metagenomics and serum metabolomics. We integrate these data using metabolic modeling and construct an integrative correlation network giving insight into key microbial species linked with disease severity, GI dysfunction, and age of patients with PD. Functional analysis reveals an increased microbial capability to degrade mucin and host glycans in PD. Personalized community-level metabolic modeling reveals the microbial contribution to folate deficiency and hyperhomocysteinemia observed in patients with PD. The metabolic modeling approach could be applied to uncover gut microbial metabolic contributions to PD pathophysiology.
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Affiliation(s)
- Dorines Rosario
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Gholamreza Bidkhori
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Janis Bedarf
- Department of Neurology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany; Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Digital Biology, Earlham Institute, Norwich, Norwich Research Park, Norwich NR4 7UZ, Norfolk, UK
| | | | - Mathias Uhlen
- Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden
| | | | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, Venusberg Campus 1, 53127 Bonn, Germany; German Centre for Neurodegenerative Disease Research (DZNE), 53127 Bonn, Germany
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK; Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden.
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK; Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, 171 65 Solna, Stockholm, Sweden.
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