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      Dietary butyrate ameliorates metabolic health associated with selective proliferation of gut Lachnospiraceae bacterium 28-4

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          Abstract

          Short-chain fatty acids, including butyrate, have multiple metabolic benefits in individuals who are lean but not in individuals with metabolic syndrome, with the underlying mechanisms still being unclear. We aimed to investigate the role of gut microbiota in the induction of metabolic benefits of dietary butyrate. We performed antibiotic-induced microbiota depletion of the gut and fecal microbiota transplantation (FMT) in APOE*3-Leiden.CETP mice, a well-established translational model for developing human-like metabolic syndrome, and revealed that dietary butyrate reduced appetite and ameliorated high-fat diet–induced (HFD-induced) weight gain dependent on the presence of gut microbiota. FMT from butyrate-treated lean donor mice, but not butyrate-treated obese donor mice, into gut microbiota–depleted recipient mice reduced food intake, attenuated HFD-induced weight gain, and improved insulin resistance. 16S rRNA and metagenomic sequencing on cecal bacterial DNA of recipient mice implied that these effects were accompanied by the selective proliferation of Lachnospiraceae bacterium 28-4 in the gut as induced by butyrate. Collectively, our findings reveal a crucial role of gut microbiota in the beneficial metabolic effects of dietary butyrate as strongly associated with the abundance of Lachnospiraceae bacterium 28-4.

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          Most cited references49

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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            KEGG: kyoto encyclopedia of genes and genomes.

            M Kanehisa (2000)
            KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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              FLASH: fast length adjustment of short reads to improve genome assemblies.

              Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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                Author and article information

                Contributors
                Journal
                JCI Insight
                JCI Insight
                JCI Insight
                JCI Insight
                American Society for Clinical Investigation
                2379-3708
                22 February 2023
                22 February 2023
                22 February 2023
                : 8
                : 4
                : e166655
                Affiliations
                [1 ]Department of Medicine, Division of Endocrinology, and
                [2 ]Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, Netherlands.
                [3 ]Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
                [4 ]Department of Pediatrics, University Medical Center Groningen, Groningen, Netherlands.
                [5 ]Center for Proteomics and Metabolomics,
                [6 ]Department of Medical Microbiology,
                [7 ]Center for Microbiome Analyses and Therapeutics, and
                [8 ]Department of Human Genetics, Leiden University Medical Center, Netherlands.
                [9 ]Med-X Institute, Center for Immunological and Metabolic Diseases, and Department of Endocrinology, the First Affiliated Hospital of Xi’an JiaoTong University, Xi’an Jiaotong University, Xi’an, China.
                Author notes
                Address correspondence to: Yanan Wang, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, Netherlands. Phone: 317168163; Email: Y.Wang@ 123456lumc.nl .
                Author information
                http://orcid.org/0000-0002-2852-8953
                http://orcid.org/0000-0002-3540-7877
                http://orcid.org/0000-0002-0014-5571
                http://orcid.org/0000-0002-1881-8826
                http://orcid.org/0000-0002-2040-2563
                http://orcid.org/0000-0003-1684-1894
                http://orcid.org/0000-0002-7409-2847
                http://orcid.org/0000-0002-2172-7394
                http://orcid.org/0000-0002-8455-4988
                http://orcid.org/0000-0002-0327-0458
                Article
                166655
                10.1172/jci.insight.166655
                9977501
                36810253
                670ded41-351e-4fe3-ae14-91c9178d344f
                © 2023 Li et al.

                This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 October 2022
                : 13 January 2023
                Funding
                Funded by: National Natural Science Foundation of China, https://doi.org/10.13039/501100001809;
                Award ID: 82170876,82200936
                Funded by: Leiden University Fund
                Award ID: W18307-2-53,W213045-2
                Funded by: Netherlands Organization for Scientific Research-NWO
                Award ID: 91617027
                Funded by: Netherlands Organization for Health Research and Development-ZonMW
                Award ID: 435004007
                Funded by: Dutch Heart Foundation
                Award ID: CVON-GENIUS-2,CVON-IN-CONTROL II,2009T038
                Categories
                Research Article

                endocrinology,microbiology,obesity
                endocrinology, microbiology, obesity

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