Stanford Advisors


All Publications


  • Captivity reduces diversity and shifts composition of the Brown Kiwi microbiome. Animal microbiome San Juan, P. A., Castro, I., Dhami, M. K. 2021; 3 (1): 48

    Abstract

    BACKGROUND: Captive rearing is often critical for animals that are vulnerable to extinction in the wild. However, few studies have investigated the extent to which captivity impacts hosts and their gut microbiota, despite mounting evidence indicating that host health is affected by gut microbes. We assessed the influence of captivity on the gut microbiome of the Brown Kiwi (Apteryx mantelli), a flightless bird endemic to New Zealand. We collected wild (n=68) and captive (n=38) kiwi feces at seven sites on the north island of New Zealand.RESULTS: Using bacterial 16S rRNA and fungal ITS gene profiling, we found that captivity was a significant predictor of the kiwi gut bacterial and fungal communities. Captive samples had lower microbial diversity and different composition when compared to wild samples. History of coccidiosis, a gut parasite primarily affecting captive kiwi, showed a marginally significant effect.CONCLUSIONS: Our findings demonstrate captivity's potential to shape the Brown Kiwi gut microbiome, that warrant further investigation to elucidate the effects of these differences on health.

    View details for DOI 10.1186/s42523-021-00109-0

    View details for PubMedID 34238378

  • Land-use change has host-specific influences on avian gut microbiomes. The ISME journal San Juan, P. A., Hendershot, J. N., Daily, G. C., Fukami, T. 2019

    Abstract

    Human modification of the environment, particularly through land-use change, often reduces animal species diversity. However, the effect of land-use change on the gut microbiome of wildlife in human-dominated landscapes is not well understood despite its potential consequences for host health. We sought to quantify the effect of land-use change on wild bird gut microbiomes in a countryside landscape in Costa Rica, comprising a range of habitat types, ranging from primary and secondary forests to diversified and monoculture farms. We collected 280 fresh fecal samples from individuals belonging to six common species of saltator, thrushes, and warblers at 24 sites across this land-use gradient. Through 16S rRNA community profiling, we found that bacterial species composition responded to host species identity more strongly than to habitat type. In addition, we found evidence that habitat type affected microbial composition only for two of the six bird species. Our findings indicate that some host species and their microbiota may be more vulnerable to human disturbances than others.

    View details for DOI 10.1038/s41396-019-0535-4

    View details for PubMedID 31624349

  • A global test of ecoregions (vol 2, pg 1889, 2018) NATURE ECOLOGY & EVOLUTION Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. L., Routh, D., San Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2019; 3 (4): 708
  • Author Correction: A global test of ecoregions. Nature ecology & evolution Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J. N., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. M., Routh, D., Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2019

    Abstract

    The original paper was published without unique DOIs for GBIF occurrence downloads. These have now been inserted as references 70-76, and the error has been corrected in the PDF and HTML versions of the article.

    View details for PubMedID 30858593

  • A global test of ecoregions NATURE ECOLOGY & EVOLUTION Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. L., Routh, D., San Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2018; 2 (12): 1889–96
  • A global test of ecoregions. Nature ecology & evolution Smith, J. R., Letten, A. D., Ke, P., Anderson, C. B., Hendershot, J. N., Dhami, M. K., Dlott, G. A., Grainger, T. N., Howard, M. E., Morrison, B. M., Routh, D., San Juan, P. A., Mooney, H. A., Mordecai, E. A., Crowther, T. W., Daily, G. C. 2018

    Abstract

    A foundational paradigm in biological and Earth sciences is that our planet is divided into distinct ecoregions and biomes demarking unique assemblages of species. This notion has profoundly influenced scientific research and environmental policy. Given recent advances in technology and data availability, however, we are now poised to ask whether ecoregions meaningfully delimit biological communities. Using over 200 million observations of plants, animals and fungi we show compelling evidence that ecoregions delineate terrestrial biodiversity patterns. We achieve this by testing two competing hypotheses: the sharp-transition hypothesis, positing that ecoregion borders divide differentiated biotic communities; and the gradual-transition hypothesis, proposing instead that species turnover is continuous and largely independent of ecoregion borders. We find strong support for the sharp-transition hypothesis across all taxa, although adherence to ecoregion boundaries varies across taxa. Although plant and vertebrate species are tightly linked to sharp ecoregion boundaries, arthropods and fungi show weaker affiliations to this set of ecoregion borders. Our results highlight the essential value of ecological data for setting conservation priorities and reinforce the importance of protecting habitats across as many ecoregions as possible. Specifically, we conclude that ecoregion-based conservation planning can guide investments that simultaneously protect species-, community- and ecosystem-level biodiversity, key for securing Earth's life support systems into the future.

    View details for PubMedID 30397301