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      The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice

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          Abstract

          Interactions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induce monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles. A composite classification score calculated from the observed alterations in fatty acid profiles in germfree mice clearly differentiates antibiotic-treated mice from untreated controls with high sensitivity. Mechanistic investigations reveal that acetate originating from gut microbial degradation of dietary fiber serves as precursor for hepatic synthesis of C16 and C18 fatty acids and their related glycerophospholipid species that are also released into the circulation.

          Abstract

          The role of the gut microbiota in hepatic lipid metabolism is controversial and incompletely understood. Here the authors perform multi-omics analyses of altered lipid metabolic processes in germ-free and specific pathogen-free mice, revealing how the gut microbiota affects hepatic fatty acid desaturation and elongation.

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          Most cited references39

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          Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides.

          Resistant starch (RS) is starch and products of its small intestinal digestion that enter the large bowel. It occurs for various reasons including chemical structure, cooking of food, chemical modification, and food mastication. Human colonic bacteria ferment RS and nonstarch polysaccharides (NSP; major components of dietary fiber) to short-chain fatty acids (SCFA), mainly acetate, propionate, and butyrate. SCFA stimulate colonic blood flow and fluid and electrolyte uptake. Butyrate is a preferred substrate for colonocytes and appears to promote a normal phenotype in these cells. Fermentation of some RS types favors butyrate production. Measurement of colonic fermentation in humans is difficult, and indirect measures (e.g., fecal samples) or animal models have been used. Of the latter, rodents appear to be of limited value, and pigs or dogs are preferable. RS is less effective than NSP in stool bulking, but epidemiological data suggest that it is more protective against colorectal cancer, possibly via butyrate. RS is a prebiotic, but knowledge of its other interactions with the microflora is limited. The contribution of RS to fermentation and colonic physiology seems to be greater than that of NSP. However, the lack of a generally accepted analytical procedure that accommodates the major influences on RS means this is yet to be established.
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            Proresolving lipid mediators and mechanisms in the resolution of acute inflammation.

            Inflammatory responses, like all biological cascades, are shaped by a delicate balance between positive and negative feedback loops. It is now clear that in addition to positive and negative checkpoints, the inflammatory cascade rather unexpectedly boasts an additional checkpoint, a family of chemicals that actively promote resolution and tissue repair without compromising host defense. Indeed, the resolution phase of inflammation is just as actively orchestrated and carefully choreographed as its induction and inhibition. In this review, we explore the immunological consequences of omega-3-derived specialized proresolving mediators (SPMs) and discuss their place within what is currently understood of the role of the arachidonic acid-derived prostaglandins, lipoxins, and their natural C15-epimers. We propose that treatment of inflammation should not be restricted to the use of inhibitors of the acute cascade (antagonism) but broadened to take account of the enormous therapeutic potential of inducers (agonists) of the resolution phase of inflammation.
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              Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.

              "Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.
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                Author and article information

                Contributors
                jak2043@med.cornell.edu
                josef.ecker@tum.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                14 September 2018
                14 September 2018
                2018
                : 9
                : 3760
                Affiliations
                [1 ]ISNI 0000 0004 0483 2525, GRID grid.4567.0, Institute of Computational Biology, , Helmholtz Zentrum München, ; Neuherberg, 85764 Germany
                [2 ]ISNI 0000 0000 9194 7179, GRID grid.411941.8, Present Address: Institute of Clinical Chemistry, , Universitätsklinikum Regensburg, ; Regensburg, 93053 Germany
                [3 ]ISNI 0000 0000 8653 1507, GRID grid.412301.5, Functional Microbiome Research Group, Institute of Medical Microbiology, , Universitätsklinikum Aachen, ; Aachen, 52074 Germany
                [4 ]ISNI 0000000123222966, GRID grid.6936.a, ZIEL Institute for Food and Health, , Technische Universität München (TUM), ; Freising, 85354 Germany
                [5 ]ISNI 0000000123222966, GRID grid.6936.a, Ernährung und Immunologie, , Technische Universität München (TUM), ; Freising, 85354 Germany
                [6 ]ISNI 0000000123222966, GRID grid.6936.a, Ernährungsphysiologie, , Technische Universität München (TUM), ; Freising, 85354 Germany
                [7 ]GRID grid.7490.a, Research Group Microbial Immune Regulation, , Helmholtz Centre for Infection Research, ; Braunschweig, 38124 Germany
                [8 ]ISNI 0000000123222966, GRID grid.6936.a, Proteomics and Bioanalytics, , Technische Universität München (TUM), ; Freising, 85354 Germany
                [9 ]GRID grid.452622.5, German Center for Diabetes Research (DZD), ; Neuherberg, 85764 Germany
                [10 ]ISNI 0000 0001 2312 1970, GRID grid.5132.5, Department of Analytical Biosciences, Leiden Academic Centre for Drug Research, , Leiden University, ; Leiden, 2333 Netherlands
                [11 ]ISNI 000000041936877X, GRID grid.5386.8, Present Address: Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, ; New York, 10021 USA
                Author information
                http://orcid.org/0000-0003-4886-0811
                http://orcid.org/0000-0003-0185-1459
                http://orcid.org/0000-0001-9321-2069
                http://orcid.org/0000-0002-9094-1677
                http://orcid.org/0000-0003-4734-3791
                Article
                5767
                10.1038/s41467-018-05767-4
                6138742
                30218046
                c3ef4f62-be9e-488e-bd3d-138b48b8981c
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 October 2017
                : 5 July 2018
                : 25 July 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);
                Award ID: LI 923/4-1
                Award ID: STR 1343/2
                Award ID: EC 453/1-1
                Award ID: EC 453/2-1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100004963, EC | Seventh Framework Programme (European Union Seventh Framework Programme);
                Award ID: 613979
                Award ID: 305280
                Award Recipient :
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