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      Naringin Attenuates High Fat Diet Induced Non-alcoholic Fatty Liver Disease and Gut Bacterial Dysbiosis in Mice

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          Abstract

          The incidence of non-alcoholic fatty liver disease (NAFLD) is rising annually, and emerging evidence suggests that the gut bacteria plays a causal role in NAFLD. Naringin, a natural flavanone enriched in citrus fruits, is reported to reduce hepatic lipid accumulation, but to date, no investigations have examined whether the benefits of naringin are associated with the gut bacteria. Thus, we investigated whether the antilipidemic effects of naringin are related to modulating the gut bacteria and metabolic functions. In this study, C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks, then fed an HFD with or without naringin administration for another 8 weeks. Naringin intervention reduced the body weight gain, liver lipid accumulation, and lipogenesis and attenuated plasma biochemical parameters in HFD-fed mice. Gut bacteria analysis showed that naringin altered the community compositional structure of the gut bacteria characterized by increased benefits and fewer harmful bacteria. Additionally, Spearman’s correlation analysis showed that at the genus level, Allobaculum, Alloprevotella, Butyricicoccus, Lachnospiraceae_NK4A136_group, Parasutterella and uncultured_bacterium_f_Muribaculaceae were negatively correlated and Campylobacter, Coriobacteriaceae_UCG-002, Faecalibaculum and Fusobacterium were positively correlated with serum lipid levels. These results strongly suggest that naringin may be used as a potential agent to prevent gut dysbiosis and alleviate NAFLD.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              Linking long-term dietary patterns with gut microbial enterotypes.

              Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                13 November 2020
                2020
                : 11
                : 585066
                Affiliations
                [1] 1The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences , Beijing, China
                [2] 2National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences , Beijing, China
                Author notes

                Edited by: Keshab Chandra Mondal, Vidyasagar University, India

                Reviewed by: Kanthi Kiran Kondepudi, National Agri-Food Biotechnology Institute, India; SR Joshi, North-Eastern Hill University, India

                *Correspondence: Jun Dong, jun_dong@ 123456263.net

                This article was submitted to Food Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2020.585066
                7691324
                33281780
                2e75e86d-1033-4760-8530-17f437ad7e50
                Copyright © 2020 Mu, Zhou, Yang, Zeng, Li, Zhang, Tang, Li, Wang, Shen, Huang, Dou and Dong.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 19 July 2020
                : 26 October 2020
                Page count
                Figures: 9, Tables: 0, Equations: 0, References: 69, Pages: 15, Words: 0
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 81672075
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                citrus fruits,lipogenesis,gut dysbiosis,high-fat diet,non-alcoholic fatty liver disease

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