• A refined microbiome 'fingerprint' metho

    From ScienceDaily@1:317/3 to All on Wed Apr 27 22:30:50 2022
    A refined microbiome 'fingerprint' method tracks sub-strain variants of
    a single gut microbe strain
    An absence of sub-strain variation over a short period was seen in sick patients, which may signal impending gut dysbiosis

    Date:
    April 27, 2022
    Source:
    University of Alabama at Birmingham
    Summary:
    A previously developed a microbiome 'fingerprint' method that
    identifies single strains of particular gut bacteria through
    analysis of metagenomics data from fecal samples, has been
    refined to include looking for single-nucleotide variants in the
    KEGG metabolic pathways of a particular strain. This magnified
    analysis shows a short-term difference in sub-strain dynamics of
    two Bacteroides species between healthy individuals and hospitalized
    COVID-19 patients.



    FULL STORY ========================================================================== Casey D. Morrow, Ph.D., and colleagues at the University of Alabama
    at Birmingham previously developed a microbiome "fingerprint" method
    called WSS that identifies single strains of particular gut bacteria,
    through analysis of metagenomics data from fecal samples. They have
    shown that particular strains in adults tend to remain stable over time,
    unless perturbed by events like antibiotics or obesity surgery. They also
    saw that a donor fecal transplant strain given to treat drug-resistant Clostridium difficile infections persisted in the recipient for as long
    as two years after the transplant.


    ========================================================================== Morrow and Hyunmin Koo, Ph.D., refined the fingerprint method to include looking for single-nucleotide variants in KEGG metabolic pathways of a particular strain. These variants can identify sub-strains of a single
    strain identified by WSS. To look at sub-strains of a Bacteroides vulgatus strain, for example, Morrow and Koo examined 23 different KEGG metabolic pathways present in that bacteria.

    They have now applied this magnified analysis to monitor changes in
    sub-strains over shorter periods of time, days or weeks, in two key gut bacteria -- B.

    vulgatus and Bacteroides uniformis. Comparing a small number of healthy individuals and hospitalized COVID-19 patients, they see a difference
    in sub- strain dynamics that they say foreshadows a slowing down of the intrinsic rates of strain variation in the sick patients. This slowing
    could eventually lead to a dysbiosis in the microbial strain community
    that may portend a shift in the dominant strains of the gut microbiome.

    Both of the Bacteroides species are found in high abundance in the gut
    flora, and they may be keystone species, organisms that help define an
    entire ecosystem.

    Koo and Morrow's study, "Early indicators of microbial strain dysbiosis
    in the human gastrointestinal microbial community of certain healthy
    humans and hospitalized COVID?19 patients," is published in the journal Scientific Reports.

    Koo and Morrow first analyzed previously published metagenomics data
    from 41 individuals sampled one year apart and 11 individuals sampled
    90 days apart.

    They looked at a single dominant strain of B. vulgatus in each individual
    at the two time points to see if they had showed different KEGG metabolic
    sub- strain patterns, as detected from analysis of single-nucleotide
    variants in KEGG metabolic pathways, or PKS. In general, most showed
    a different sub-strain PKS pattern between the two time points of each individual.



    ==========================================================================
    The UAB researchers then analyzed previously published metagenomics data
    from six healthy individuals sampled every few days over three to 10
    weeks, again analyzing sub-strains by single-nucleotide variants in 23
    KEGG metabolic pathways. Three individuals showed a different sub-strain
    at every time point, while three showed sub-strains had PKS patterns
    that appeared, disappeared and reappeared at different time points.

    Shared PKS patterns were also seen in two of three hospitalized COVID-19 patients who were sampled multiple times.

    "We suggest that gut microbial communities under stress, such as those
    found in COVID-19 hospitalized patients, might be in a state indicating
    the potential shift in which the dominant strain would be outcompeted by
    a minor strain," Koo said. "Disruptions of the gut microbial community resulting from a strain variation might, in turn, alter the community
    structure and impact the functions in metabolism and colonization
    resistance." "One of the features of a complex biological system is
    that, as it approaches a critical transition, there is a slowing down
    of the intrinsic rates of change," Morrow said. "The system enters
    a condition that is related to autocorrelation, where the patterns
    would be repeated between time points. It is possible that the shared
    KEGG metabolic pathway clusters represent a state of autocorrelation
    in the gut microbial strain community that portends a strain change."
    Support came from the Marnix E. Heersink School of Medicine at UAB.

    Morrow is a professor emeritus of the UAB Department of Cell,
    Developmental and Integrative Biology, and Koo is a bioinformatician in
    the UAB Department of Genetics.

    The KEGG database is an acronym for the Kyoto Encyclopedia of Genes
    and Genomes.


    ========================================================================== Story Source: Materials provided by
    University_of_Alabama_at_Birmingham. Original written by Jeff
    Hansen. Note: Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Hyunmin Koo, Casey D. Morrow. Early indicators of microbial strain
    dysbiosis in the human gastrointestinal microbial
    community of certain healthy humans and hospitalized
    COVID-19 patients. Scientific Reports, 2022; 12 (1) DOI:
    10.1038/s41598-022-10472-w ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/04/220427154104.htm

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