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      Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations

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          Abstract

          Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.

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          The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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            Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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              Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

              A 16S rRNA gene database ( http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .
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                Author and article information

                Journal
                Metabolites
                Metabolites
                metabolites
                Metabolites
                MDPI
                2218-1989
                15 January 2021
                January 2021
                : 11
                : 1
                : 55
                Affiliations
                [1 ]Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; partho.sen@ 123456utu.fi (P.S.); marina.amaral@ 123456utu.fi (M.A.A.); henrique.carachoribeiro@ 123456utu.fi (H.C.R.); pemarau@ 123456utu.fi (P.R.); matej.oresic@ 123456utu.fi (M.O.)
                [2 ]School of Medical Sciences, Orebro University, 702 81 Orebro, Sweden
                [3 ]Department of Chemistry, Orebro University, 702 81 Orebro, Sweden; Tuulia.Hyotylainen@ 123456oru.se
                [4 ]Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
                Author notes
                Author information
                https://orcid.org/0000-0003-0475-2763
                https://orcid.org/0000-0003-4241-8950
                https://orcid.org/0000-0002-1389-8302
                Article
                metabolites-11-00055
                10.3390/metabo11010055
                7830997
                33467644
                8104b4d1-1205-4ab3-9e5a-cf12b26a4627
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 16 December 2020
                : 12 January 2021
                Categories
                Review

                microbiome,lipidomics,metabolomics,gut,lipids
                microbiome, lipidomics, metabolomics, gut, lipids

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