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      Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study

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          ABSTRACT

          Nonalcoholic fatty liver disease (NAFLD) is a risk factor for liver cancer and prevalence varies by ethnicity. Along with genetic and lifestyle factors, the gut microbiome (GM) may contribute to NAFLD and its progression to advanced liver disease. Our cross-sectional analysis assessed the association of the GM with hepatic adiposity among African American, Japanese American, White, Latino, and Native Hawaiian participants in the Multiethnic Cohort. We used MRI to measure liver fat and determine nonalcoholic fatty liver disease (NAFLD) status (n = 511 cases) in 1,544 participants, aged 60–77 years, with 12–53% overall adiposity (BMI of 17.8–46.2 kg/m 2). The GM was measured by 16S rRNA gene sequencing and, on a subset, by metagenomic sequencing. Alpha diversity was lower overall with NAFLD and in certain ethnicities (African Americans, Whites, and Latinos). In models regressing genus on NAFLD status, 62 of 149 genera (40%) exhibited a significant interaction between NAFLD and ethnicity stratified analysis found 69 genera significantly associated with NAFLD in at least one ethnic group. No single genus was significantly associated with NAFLD across all ethnicities. In contrast, the same bacterial metabolic pathways were over-represented in participants with NAFLD regardless of ethnicity. Imputed secondary bile acid and carbohydrate pathways were associated with NAFLD, the latter of which was corroborated by metagenomics, although different genera in different ethnicities were associated with these pathways. Overall, we found that NAFLD was associated with altered bacterial composition and metabolism, and that bacterial endotoxin, assessed by plasma lipopolysaccharide binding protein (LBP), may mediate liver fat-associated systemic inflammation in a manner that seems to vary by ethnicity.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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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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              QIIME allows analysis of high-throughput community sequencing data.

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                Author and article information

                Journal
                Gut Microbes
                Gut Microbes
                Gut Microbes
                Taylor & Francis
                1949-0976
                1949-0984
                7 September 2021
                2021
                7 September 2021
                : 13
                : 1
                : 1965463
                Affiliations
                [a ]Public Health Sciences, Fred Hutchinson Cancer Research Center; , Seattle, Washington, U.S.A
                [b ]Clinical Research Division, Fred Hutchinson Cancer Research Center; , Seattle, Washington, U.S.A
                [c ]Preventive Medicine, Keck School Of Medicine, University Of Southern California; , Los Angeles, California, U.S.A
                [d ]John A. Burns School Of Medicine, University Of Hawaii; , Honolulu, Hawaii, U.S.A
                [e ]University Of Hawaii Cancer Center, University Of Hawaii; , Honolulu, Hawaii, U.S.A
                [f ]Keck School Of Medicine, University Of Southern California; , Los Angeles, California, U.S.A
                [g ]School Of Medicine, University Of California San Francisco; , San Francisco, California, U.S.A
                [h ]Department Of Medicine, Brigham And Women’s Hospital And Harvard Medical School; , Boston, Massachusetts, U.S.A
                Author notes
                CONTACT Meredith A. J. Hullar mhullar@ 123456fredhutch.org Public Health Sciences, Fred Hutchinson Cancer Research Center; , Seattle, Washington, U.S.A.
                [&]

                These authors contributed equally as co-senior author

                Author information
                https://orcid.org/0000-0002-5322-9568
                https://orcid.org/0000-0001-8465-1588
                https://orcid.org/0000-0002-3016-2081
                https://orcid.org/0000-0003-4132-2893
                https://orcid.org/0000-0001-5013-980X
                https://orcid.org/0000-0001-6221-7190
                https://orcid.org/0000-0003-2717-3780
                Article
                1965463
                10.1080/19490976.2021.1965463
                8425768
                34491886
                5ae0d663-b699-4589-b8ba-ce7f44a167c3
                © 2021 The Author(s). Published with license by Taylor & Francis Group, LLC.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 3, Tables: 2, References: 100, Pages: 1
                Categories
                Research Article
                Research Paper

                Microbiology & Virology
                nonalcoholic fatty liver disease (nafld),inflammation,hepatocellular carcinoma,chronic liver disease,ethnic groups,genetics,diabetes,metabolic syndrome

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