Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos taurus breeds and basal diets

MD Auffret, R Stewart, RJ Dewhurst, C-A Duthie, JA Rooke, RJ Wallace, TC Freeman, TJ Snelling, M Watson, R Roehe

    Research output: Contribution to journalArticle

    10 Citations (Scopus)

    Abstract

    Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP>0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments.
    Original languageEnglish
    Article number2642
    Number of pages15
    JournalFrontiers in Microbiology
    Volume8
    Early online date9 Jan 2018
    DOIs
    Publication statusFirst published - 9 Jan 2018

    Fingerprint

    Rumen
    Methane
    Biomarkers
    Diet
    Metagenomics
    Genes
    Methylomonas
    Microbial Genetics
    Volatile Fatty Acids
    Microbiota
    Firearms
    Least-Squares Analysis
    Genetic Markers
    Reproducibility of Results
    Carbon
    Gases
    Phenotype
    Lipids
    Population

    Bibliographical note

    1030565

    Keywords

    • Biomarkers
    • DIETS
    • Metagenomics
    • Methane
    • Rumen microbiome

    Cite this

    @article{018047c3c25b47149922f50682df880a,
    title = "Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos taurus breeds and basal diets",
    abstract = "Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP>0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments.",
    keywords = "Biomarkers, DIETS, Metagenomics, Methane, Rumen microbiome",
    author = "MD Auffret and R Stewart and RJ Dewhurst and C-A Duthie and JA Rooke and RJ Wallace and TC Freeman and TJ Snelling and M Watson and R Roehe",
    note = "1030565",
    year = "2018",
    month = "1",
    day = "9",
    doi = "10.3389/fmicb.2017.02642",
    language = "English",
    volume = "8",
    journal = "Frontiers in Microbiology",
    issn = "1664-302X",
    publisher = "Frontiers Media",

    }

    Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos taurus breeds and basal diets. / Auffret, MD; Stewart, R; Dewhurst, RJ; Duthie, C-A; Rooke, JA; Wallace, RJ; Freeman, TC; Snelling, TJ; Watson, M; Roehe, R.

    In: Frontiers in Microbiology, Vol. 8, 2642, 09.01.2018.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos taurus breeds and basal diets

    AU - Auffret, MD

    AU - Stewart, R

    AU - Dewhurst, RJ

    AU - Duthie, C-A

    AU - Rooke, JA

    AU - Wallace, RJ

    AU - Freeman, TC

    AU - Snelling, TJ

    AU - Watson, M

    AU - Roehe, R

    N1 - 1030565

    PY - 2018/1/9

    Y1 - 2018/1/9

    N2 - Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP>0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments.

    AB - Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP>0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments.

    KW - Biomarkers

    KW - DIETS

    KW - Metagenomics

    KW - Methane

    KW - Rumen microbiome

    U2 - 10.3389/fmicb.2017.02642

    DO - 10.3389/fmicb.2017.02642

    M3 - Article

    C2 - 29375511

    VL - 8

    JO - Frontiers in Microbiology

    JF - Frontiers in Microbiology

    SN - 1664-302X

    M1 - 2642

    ER -