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  1. Article ; Online: The human microbiome, global health and the Sustainable Development Goals: opportunities and challenges.

    O'Toole, Paul W / Paoli, Max

    Nature reviews. Microbiology

    2023  Volume 21, Issue 10, Page(s) 624–625

    MeSH term(s) Humans ; Global Health ; Sustainable Development ; Public Health ; Microbiota
    Language English
    Publishing date 2023-06-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-023-00924-z
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  2. Article ; Online: Microbe Profile: The

    Walter, Jens / O'Toole, Paul W

    Microbiology (Reading, England)

    2023  Volume 169, Issue 12

    MeSH term(s) Lactobacillaceae ; Probiotics
    Language English
    Publishing date 2023-12-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.001414
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  3. Article ; Online: Human microbiome variance is underestimated.

    Shanahan, Fergus / Ghosh, Tarini S / O'Toole, Paul W

    Current opinion in microbiology

    2023  Volume 73, Page(s) 102288

    Abstract: Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living ... ...

    Abstract Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living in socioeconomically developed countries. This may have skewed the interpretation of microbiome variance and its relationship to health and disease. Moreover, striking under-representation of minority groups in microbiome studies is a missed opportunity to assess context, history and the changing nature of the microbiome in relation to the risk of disease. Therefore, we focus here on areas of recent progress - ageing and ethnicity - both of which contribute to microbiome variance with particular lessons for the promise of microbiome-based diagnostics and therapeutics.
    MeSH term(s) Humans ; Microbiota ; Life Style ; Aging
    Language English
    Publishing date 2023-03-06
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2023.102288
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  4. Article ; Online: The gut microbiome as a modulator of healthy ageing.

    Ghosh, Tarini Shankar / Shanahan, Fergus / O'Toole, Paul W

    Nature reviews. Gastroenterology & hepatology

    2022  Volume 19, Issue 9, Page(s) 565–584

    Abstract: The gut microbiome is a contributory factor in ageing-related health loss and in several non-communicable diseases in all age groups. Some age-linked and disease-linked compositional and functional changes overlap, while others are distinct. In this ... ...

    Abstract The gut microbiome is a contributory factor in ageing-related health loss and in several non-communicable diseases in all age groups. Some age-linked and disease-linked compositional and functional changes overlap, while others are distinct. In this Review, we explore targeted studies of the gut microbiome of older individuals and general cohort studies across geographically distinct populations. We also address the promise of the targeted restoration of microorganisms associated with healthier ageing.
    MeSH term(s) Gastrointestinal Microbiome ; Healthy Aging ; Humans
    Language English
    Publishing date 2022-04-25
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2493722-8
    ISSN 1759-5053 ; 1759-5045
    ISSN (online) 1759-5053
    ISSN 1759-5045
    DOI 10.1038/s41575-022-00605-x
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  5. Article ; Online: Toward an improved definition of a healthy microbiome for healthy aging.

    Ghosh, Tarini Shankar / Shanahan, Fergus / O'Toole, Paul W

    Nature aging

    2022  Volume 2, Issue 11, Page(s) 1054–1069

    Abstract: The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including ... ...

    Abstract The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance. We analyzed 21,000 fecal microbiomes from seven data repositories, across five continents spanning participant ages 18-107 years, revealing that microbiome diversity and uniqueness correlate with aging, but not healthy aging. Among summary statistics tested, only Kendall uniqueness accurately reflects loss of the core microbiome and the abundance and ranking of disease-associated and health-associated taxa. Increased abundance of these disease-associated taxa and depletion of a coabundant subset of health-associated taxa are a generic feature of aging. These alterations are stronger correlates of unhealthy aging than most microbiome summary statistics and thus help identify better targets for therapeutic modulation of the microbiome.
    MeSH term(s) Humans ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Bacteria ; Microbiota ; Gastrointestinal Microbiome ; Aging ; Feces
    Language English
    Publishing date 2022-11-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2662-8465
    ISSN (online) 2662-8465
    DOI 10.1038/s43587-022-00306-9
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  6. Article ; Online: Human microbiome variance is underestimated

    Shanahan, Fergus / Ghosh, Tarini S. / O'Toole, Paul W

    Current Opinion in Microbiology. 2023 June, v. 73 p.102288-

    2023  

    Abstract: Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living ... ...

    Abstract Most of the variance in the human microbiome remains unexplained. Although an extensive list of individual lifestyles shaping the microbiome has been identified, important gaps in knowledge persist. Most human microbiome data are from individuals living in socioeconomically developed countries. This may have skewed the interpretation of microbiome variance and its relationship to health and disease. Moreover, striking under-representation of minority groups in microbiome studies is a missed opportunity to assess context, history and the changing nature of the microbiome in relation to the risk of disease. Therefore, we focus here on areas of recent progress - ageing and ethnicity - both of which contribute to microbiome variance with particular lessons for the promise of microbiome-based diagnostics and therapeutics.
    Keywords diagnostic techniques ; humans ; microbiology ; microbiome ; nationalities and ethnic groups ; risk ; therapeutics ; variance
    Language English
    Dates of publication 2023-06
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Pre-press version ; Use and reproduction
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2023.102288
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  7. Article ; Online: Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables.

    Yap, Min / O'Sullivan, Orla / O'Toole, Paul W / Sheehan, Jeremiah J / Fenelon, Mark A / Cotter, Paul D

    mSystems

    2024  Volume 9, Issue 4, Page(s) e0129023

    Abstract: Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk ... ...

    Abstract Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (
    Importance: The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.
    MeSH term(s) Female ; Animals ; Milk ; Seasons ; Bacteria ; Microbiota ; Metagenome
    Language English
    Publishing date 2024-03-06
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN (online) 2379-5077
    DOI 10.1128/msystems.01290-23
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  8. Article ; Online: Translating the Microbiome: What's the Target?

    O'Toole, Paul W / Ghosh, Tarini Shankar / Goswami, Sourav / Manghi, Paolo / Segata, Nicola / Shanahan, Fergus

    Gastroenterology

    2023  Volume 165, Issue 2, Page(s) 317–319

    MeSH term(s) Humans ; Microbiota
    Language English
    Publishing date 2023-04-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80112-4
    ISSN 1528-0012 ; 0016-5085
    ISSN (online) 1528-0012
    ISSN 0016-5085
    DOI 10.1053/j.gastro.2023.04.008
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  9. Article ; Online: Geographical and Seasonal Analysis of the Honeybee Microbiome

    Almeida, Eduardo L. / Ribiere, Celine / Frei, Werner / Kenny, Denis / Coffey, Mary F. / O’Toole, Paul W.

    Microb Ecol. 2023 Feb., v. 85, no. 2 p.765-778

    2023  

    Abstract: We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the ... ...

    Abstract We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June–July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.
    Keywords apiaries ; forage ; honey ; honey bees ; microbiome ; worker bees ; Ireland
    Language English
    Dates of publication 2023-02
    Size p. 765-778.
    Publishing place Springer US
    Document type Article ; Online
    ZDB-ID 1462065-0
    ISSN 1432-184X ; 0095-3628
    ISSN (online) 1432-184X
    ISSN 0095-3628
    DOI 10.1007/s00248-022-01986-x
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  10. Article ; Online: Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease.

    Ghosh, Tarini Shankar / Arnoux, Jerome / O'Toole, Paul W

    Gut microbes

    2020  Volume 12, Issue 1, Page(s) 1–19

    Abstract: Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of ... ...

    Abstract Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli - food, environment, the gut - is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by
    MeSH term(s) Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Body Mass Index ; Child ; Child, Preschool ; Diabetes Mellitus, Type 2/microbiology ; Diet ; Disease ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Geography ; Health ; Humans ; Infant ; Inflammatory Bowel Diseases/microbiology ; Lactobacillus/classification ; Lactobacillus/genetics ; Lactobacillus/growth & development ; Lactobacillus/isolation & purification ; Liver Diseases/microbiology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Sex Factors ; Young Adult
    Language English
    Publishing date 2020-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1949-0984
    ISSN (online) 1949-0984
    DOI 10.1080/19490976.2020.1822729
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