Browsing by Author "Chopyk, Jessica"
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Item Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018(Springer Nature, 2018-11-05) Meisel, Jacquelyn S.; Nasko, Daniel J.; Brubach, Brian; Cepeda-Espinoza, Victoria; Chopyk, Jessica; Corrada-Bravo, Héctor; Fedarko, Marcus; Ghurye, Jay; Javkar, Kiran; Olson, Nathan D.; Shah, Nidhi; Allard, Sarah M.; Bazinet, Adam L.; Bergman, Nicholas H.; Brown, Alexis; Caporaso, J. Gregory; Conlan, Sean; DiRuggiero, Jocelyne; Forry, Samuel P.; Hasan, Nur A.; Kralj, Jason; Luethy, Paul M.; Milton, Donald K.; Ondov, Brian D.; Preheim, Sarah; Ratnayake, Shashikala; Rogers, Stephanie M.; Rosovitz, M. J.; Sakowski, Eric G.; Schliebs, Nils Oliver; Sommer, Daniel D.; Ternus, Krista L.; Uritskiy, Gherman; Zhang, Sean X.; Pop, Mihai; Treangen, Todd J.The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.Item Diversity, dynamics, and dissemination of microbial communities in reclaimed and untreated surface waters used for agricultural irrigation(2019) Chopyk, Jessica; Sapkota, Amy R; Public and Community Health; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)High quality freshwater is a vital resource for sustaining agriculture and feeding a growing global population. Yet, due to increasing declines in groundwater, key food production regions across the world face uncertainty with regard to water availability. Nontraditional irrigation water sources, such as reclaimed water (advanced treated municipal wastewater) and untreated surface water (e.g. creeks, ponds, and brackish rivers), may contribute to sustainable solutions to conserve groundwater supplies. However, the microbial community composition and dynamics within these water sources are typically poorly characterized and comparative analysis of their microbial communities are rare. Using high-throughput, cultivation-independent sequencing methodologies, this dissertation research focused on three aims: 1) exploring the functional and taxonomic features of bacteria in nontraditional irrigation water sources; 2) assessing the bacterial and viral communities of agricultural pond water in relation to seasonality; and 3) describing the dynamics, composition, and potential dissemination of irrigation water microbiota from a freshwater creek to an irrigated field. The first aim was addressed through a broad investigation of bacteria within agricultural ponds, freshwater creeks, brackish rivers, and reclamation facilities. Through metagenomic-based analyses, features of the bacterial community, such as antimicrobial resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays, were found to vary by sampling date and specific site. For the second aim, agricultural pond water was sampled over two time periods and found to harbor diverse bacteria and bacteriophage species, the abundance and composition of which were influenced by factors characteristic of the pond’s topography and seasonality. For the final aim, samples from a creek used actively for agricultural irrigation, as well as samples of pre- and post-irrigated soil, were analyzed. ARGs and virulence factors were identified in the water and soil samples, with the majority being specific to their respective environment. Moreover, analyses of CRISPR arrays from the creek samples indicated the persistence of certain bacterial lineages, as well as specific interactions between creek bacteriophage and their hosts. Overall, this research improves scientific knowledge of bacterial and viral composition, dynamics, and interactions that can be utilized to assess the suitability and safety of nontraditional irrigation water sources.Item Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens(Springer Nature, 2017-02-15) Chopyk, Jessica; Chattopadhyay, Suhana; Kulkarni, Prachi; Claye, Emma; Babik, Kelsey R.; Reid, Molly C.; Smyth, Eoghan M.; Hittle, Lauren E.; Paulson, Joseph N.; Cruz-Cano, Raul; Pop, Mihai; Buehler, Stephanie S.; Clark, Pamela I.; Sapkota, Amy R.; Mongodin, Emmanuel F.There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product. Total genomic DNA was extracted using a multi-step enzymatic and mechanical lysis protocol followed by PCR amplification of the V3-V4 hypervariable regions of the 16S rRNA gene from five cigarette products (18 cigarettes per product for a total of 90 samples): Camel Crush, user-mentholated Camel Crush, Camel Kings, custom-mentholated Camel Kings, and Newport Menthols. Sequencing was performed on the Illumina MiSeq platform and sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package. In all products, Pseudomonas was the most abundant genera and included Pseudomonas oryzihabitans and Pseudomonas putida, regardless of mentholation status. However, further comparative analysis of the five products revealed significant differences in the bacterial compositions across products. Bacterial community richness was higher among non-mentholated products compared to those that were mentholated, particularly those that were custom-mentholated. In addition, mentholation appeared to be correlated with a reduction in potential human bacterial pathogens and an increase in bacterial species resistant to harsh environmental conditions. Taken together, these data provide preliminary evidence that the mentholation of commercially available cigarettes can impact the bacterial community of these products.Item Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation(Springer Nature, 2019-04-11) Chopyk, Jessica; Kulkarni, Prachi; Nasko, Daniel J.; Bradshaw, Rhodel; Kniel, Kalmia E.; Chiu, Pei; Sharma, Manan; Sapkota, Amy R.Zero-valent iron sand filtration can remove multiple contaminants, including some types of pathogenic bacteria, from contaminated water. However, its efficacy at removing complex viral populations, such as those found in reclaimed water used for agricultural irrigation, has not been fully evaluated. Therefore, this study utilized metagenomic sequencing and epifluorescent microscopy to enumerate and characterize viral populations found in reclaimed water and zero-valent iron-sand filtered reclaimed water sampled three times during a larger greenhouse study.