• Genetics affects functions of gut microb

    From ScienceDaily@1:317/3 to All on Mon Apr 18 22:30:48 2022
    Genetics affects functions of gut microbiome

    Date:
    April 18, 2022
    Source:
    Cornell University
    Summary:
    Scientists are exploring how human genetics impacts functions of
    the gut microbiome, and are expanding awareness of the role human
    genetics plays in shaping the microbiome.



    FULL STORY ==========================================================================
    New research from Cornell scientists is exploring how human genetics
    impacts functions of the gut microbiome, and is expanding awareness of
    the role human genetics plays in shaping the microbiome.


    ==========================================================================
    The trillions of individual organisms constituting a person's gut
    microbiome greatly impact metabolic function, disease and overall
    health. What has been less clear is how and to what extent the gut
    microbiome is, in turn, shaped by the genome of its human host.

    Ilana Brito, assistant professor and Mong Family Sesquicentennial
    Faculty Fellow in the Nancy E. and Peter C. Meinig School of Biomedical Engineering, and her coauthors took a novel approach to examining host-microbiome genetic interactions and were able to show many instances
    where a human host's genetic makeup directly affected the functional performance of the gut microbiome.

    Their paper, "Collective Effects of Human Genomic Variation on Microbiome Function," was published March 9 in the journal Scientific Reports. The
    study was a cross-college collaboration that combined Brito's knowledge of
    the microbiome with faculty expertise in genetic variation and statistical methodology, respectively, from Andrew Clark, the Jacob Gould Schurman Professor of Population Genetics in the College of Arts and Sciences;
    and Martin Wells, the Charles A. Alexander Professor of Statistical
    Sciences in the Department of Information Science.

    "When a disease or phenotype is caused by a single genetic mutation it
    can be a relatively straightforward process to find the gene responsible," Brito said.

    But just as often, an entire suite of genes can interact to result
    in disease or other phenotypic expression, a much more complex
    mechanism. Within the human genome there are many sequential variations
    from person to person and even within paired chromosomes of the same
    person.

    When a variation is produced by the substitution of a single nucleotide,
    this is called single nucleotide polymorphism (SNP). Using a unique computational and modeling approach, Brito's team was able to identify
    SNPs that correlated with microbiome-associated traits, disorders and
    cancers. In other words, they were able to show direct effects of the
    human genome on the functions of the gut microbiome.



    ========================================================================== "Associating variation in the human genome with the variation in the
    gut microbiome has been tricky," Clark said, "because the human genome
    variants are correlated with each other, and can have related functions,
    and the species of bacteria in the gut are also not independent of
    each other." The novelty of the current study was to make use of this structure in the data.

    It focused on the function of the gut microbiome as opposed to the genetic makeup of each species in the agglomeration of organisms that forms the microbiome; it looked at broad collections of human genes and their effect
    on the functions of the microbiome as opposed to examining single genes;
    and it used a new type of strategy to model the distribution of functions
    and species within the human gut.

    Past models haven't been a good fit for the characteristics common to metagenomic sequencing data sets. Wells introduced the idea of using
    the Tweedie distribution -- a type of probability modeling -- to account
    for these characteristics.

    "My research group has previously applied a Tweedie modeling strategy
    in natural language processing," Wells said. "It seemed like a good fit
    here, too.

    We found that the Tweedie modeling approach was flexible enough to capture
    the mean-to-variance power relationship in the metagenomic taxa and gene abundances and was superior to the standard approaches." First author
    of the paper is Felicia New, Ph.D. '21, formerly part of Brito's lab
    group and second author is Benjamin Baer, Ph.D. '21, a Wells advisee.

    "Felicia brought the expertise on these microbes and their functions
    and human genetics, and Benjamin brought the stats background and they
    worked together to mesh their expertise and see what specific approach
    made sense," Brito said.

    "It was through this collaboration that we were to do some excellent
    work." The research was supported by a grant from the National Institutes
    of Health.


    ========================================================================== Story Source: Materials provided by Cornell_University. Original written
    by Chris Dawson, courtesy of the Cornell Chronicle. Note: Content may
    be edited for style and length.


    ========================================================================== Journal Reference:
    1. Felicia N. New, Benjamin R. Baer, Andrew G. Clark, Martin T. Wells,
    Ilana
    L. Brito. Collective effects of human genomic variation on
    microbiome function. Scientific Reports, 2022; 12 (1) DOI:
    10.1038/s41598-022-07632- 3 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/04/220418122937.htm

    --- up 7 weeks, 10 hours, 51 minutes
    * Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1:317/3)