Browsing by Author "Mihindukulasuriya, Kathie A."

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    Biogeography of the ecosystems of the healthy human body
    (Springer Nature, 2013-01-14) Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A.; La Rosa, Patricio S.; Wylie, Kristine M.; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I.; Nelson, David E.; Fortenberry, J. Dennis; Holland, Martin J.; Burr, Sarah E.; Shannon, William D.; Sodergren, Erica; Weinstock, George M.; Pediatrics, School of Medicine
    Background: Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans. Results: We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies. Conclusions: The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.
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    Exploration of bacterial community classes in major human habitats
    (Springer Nature, 2014-05-07) Zhou, Yanjiao; Mihindukulasuriya, Kathie A.; Gao, Hongyu; La Rosa, Patricio S.; Wylie, Kristine M.; Martin, John C.; Kota, Karthik; Shannon, William D.; Mitreva, Makedonka; Sodergren, Erica; Weinstock, George M.; Medical and Molecular Genetics, School of Medicine
    Background: Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project. Results: We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days. Conclusion: The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes.