Román Busó, Gabriela Paola

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    Genetic characterization of host-microbiome-pathogen dynamics in ancient Amerindians of Punta Candelero, Puerto Rico
    (2020-10-27) Román Busó, Gabriela Paola; Martínez Cruzado, Juan C.; College of Arts and Sciences - Sciences; Matchett, Ashley A.; Oleksyk, Taras K.; Department of Biology; Ramírez, Lillian
    This thesis seeks to address the deficit of ancestral human references from the tropics, specifically the Caribbean, by adding genetic (genomic and microbiomic) information from the ancient Puerto Rican Amerindian population of Punta Candelero. Ancient DNA (aDNA) methods coupled with metagenomics sequencing and analysis were used to investigate the host-microbiome-pathogen sequences in dental samples to generate a more comprehensive landscape of the genealogy and health of indigenous precolonial populations of Puerto Rico. Three aDNA extraction methods were optimized and evaluated specifically for the samples. Site-directed detection and sequencing for human host (mtDNA HVS-1) and bacterial DNA (16S rRNA) were used to determine an optimal sample for shotgun metagenomic sequencing. Shotgun sequences generated for the selected sample were analyzed using a reference-based mapping to the human genome, while unmapped sequences were searched against NCBI NR database for taxonomic classification. Results demonstrate a successful recovery of ancient DNA, although at very low concentration. A partial human mitogenome was successfully reconstructed for the selected sample and identified as C1b2 mtDNA sub-haplogroup, consistent with recent investigations of pre-contact Puerto Rican individuals. In addition, a multiple isotope analysis, including Pb isotope ratios, preliminarily verifies the sequenced individual was of local origin. Finally, the microbial composition of the sample reported here differed from that of the reported taxonomic composition for coprolites and calculi of ancient indigenous Puerto Ricans (Sorcé site, Vieques), which may suggest an increased enrichment of soil bacteria in the sample. Microbial sequences for Neglected Tropical Diseases (NTDs) and other oral and gastrointestinal pathogens of interest were detected at trace amounts, but the endogenous nature of the detected microbial sequences should be further verified and cannot yet be used to evaluate the health of the individual.