Bioinformatics Commons^™

Understanding Host-Microbe Interactions In Maize Kernel And Sweetpotato Leaf Metagenomic Profiles., Alison K. Adams

Doctoral Dissertations

Functional and quantitative metagenomic profiling remains challenging and limits our understanding of host-microbe interactions. This body of work aims to mediate these challenges by using a novel quantitative reduced representation sequencing strategy (OmeSeq-qRRS), development of a fully automated software for quantitative metagenomic/microbiome profiling (Qmatey: quantitative metagenomic alignment and taxonomic identification using exact-matching) and implementing these tools for understanding plant-microbe-pathogen interactions in maize and sweetpotato. The next generation sequencing-based OmeSeq-qRRS leverages the strengths of shotgun whole genome sequencing and costs lower that the more affordable amplicon sequencing method. The novel FASTQ data compression/indexing and enhanced-multithreading of the MegaBLAST in Qmatey allows …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

Taxonomic Classification Of Viral And Bacterial Dna Following 2021 Avian Mass Mortality Event, Tessa Baillargeon

Honors Theses and Capstones

From May through July 2021, an unusual mortality event occurred along the eastern coast and Midwest of the United States. Thousands of birds, mostly from the order Passeriformes, were part of the die-off including blue jays (Cyanocitta cristata), common grackles (Quiscalus quiscula), European starlings (Sturnus vulgaris), American robins (Turdus migratorius). Clinical signs included crusted eyes, swollen conjunctiva, otitis, seizures, and ataxia.

The New Hampshire Veterinary Diagnostic Laboratory (NHVDL) received over 100 affected birds from various collaborators throughout the United States including Washington DC, NJ, CT, MD, and OH. Given the timing and geologic …

Accurate Simulation Of Reads And Improved Strategies For Abundance Estimation Supporting Reduced Representation Sequencing For Metagenomics, Ryan Kuster

Doctoral Dissertations

Next generation sequencing has impacted all areas of biology by providing affordable investigations into some of the most complex processes underpinning life. With its ubiquitous application, there is still benefit in considering the nuances of the technology and its downstream analysis. Sequencing libraries produced by fragmenting DNA with restriction enzyme digests limit the scope of sequencing to a reduced set of genomic loci, allowing for deeper sequencing of those regions at a reduced cost per sample. These sequencing libraries have been used to determine genetic markers within populations of closely related individuals due to their sensitivity and preservation within populations. …

Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris

Electronic Thesis and Dissertation Repository

Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.

Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …

Metagenome-Wide Associations And Metabolic Modeling To Predict The Biomarkers For Colorectal Cancer, Nagavardhini Avuthu

Theses & Dissertations

Colorectal cancer (CRC) is the most common malignancy and the second most common cause of cancer-related deaths in the world. It is a multifactorial disease mediated by genetic, environmental, and lifestyle factors. Over time, the accumulation of genetic and epigenetic changes results in the activation of oncogenes and deactivation of tumor suppressor genes in the colon and rectal region which finally leads to tumor development. The gut microbiome is the main factor linking the effects of diet and environmental factors to host metabolism. Several studies showed the dysbiosis of gut microbiota in CRC patients with an increased proportion of pathogenic …

Investigation Of Microbe And Host Tissue Interactions Contributing To The Pathogenesis Of Colorectal Cancer, Ryan Chapman, Dhundy Bastola

Theses/Capstones/Creative Projects

Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The pathogenesis of this disease can fall under broad categories; however, the specific precursory mechanism of CRC pathogenesis is still unknown. Dysregulations of the gut microbiome have been identified in the CRC tissue environment. Additionally, CRC tissue gene expression has been observed to differ from that of healthy tissue. Despite these noticeable changes, few studies have directly compared the microorganism composition to the gene expression of CRC tissue. Doing so may identify whether the differentially abundant microorganisms influence the changes in gene expression. The goal of this …

Identification Of Candidate Microbial Biomarkers Of Disease And Design Of Engineered Microbial Therapeutics For The Gut Microbiome, Aura Lucia Ferreiro

McKelvey School of Engineering Theses & Dissertations

The human gut microbiome is a compositionally and functionally diverse community of microorganisms that profoundly influences the health of the host. Deep characterization of gut microbiomes via high-throughput sequencing has identified associations between the gut microbiome and disease states, and spurred development of engineered microbial therapeutics. Successful translation of these research efforts to the clinic will involve i) consideration of how engineered microbes behave and adapt in the gut, towards the implementation of biosafety mechanisms, and ii) identification and validation of microbial biomarkers of disease. This dissertation describes both investigative (Chapter 2) and engineering (Chapters 3 and 4) approaches to …

Strainiq: An N-Gram-Based Method To Identify And Quantify Microbial Communities In Metagenomic Samples, Sanjit Pandey

Theses & Dissertations

Microbes are ubiquitous in nature, and they play vital roles in various processes associated with metabolism in the human body, photosynthesis in plants, or decomposition of waste in the environment. Hence, it is essential to understand how the composition of microbial communities affects the ecosystem of different environments ranging from ocean floors to hot springs to the human body. Microbial communities present in different human body sites are of particular importance due to their implications in the cause and prevention of human diseases. The traditional approaches limit microbial research to exclusively studying species that can be successfully cultured in the …

Multi-Omic Understanding Of The Evolution Of Xenobiotic Tolerance In Bacterial Isolates And Communities, Tayte Paul Campbell

Arts & Sciences Electronic Theses and Dissertations

Xenobiotic compounds are any chemicals that are released into an environment by human action and that occur at concentrations higher than found naturally. Xenobiotics, including aromatic compounds and antibiotics, are recalcitrant to degradation because they are often toxic or mutagenic. Despite this toxicity, bacteria account for a large portion of xenobiotic degradation in the environment. Bacteria are able to adapt to these foreign chemicals, gaining increased levels of tolerance and increased rates of xenobiotic degradation. On the strain level, increased tolerance can be caused by mutations in individual cells or through the acquisition of genes from other cells. At the …

The Influence Of Conservation Tillage And Conventional Tillage On Soil Bacterial Diversity In Southern Illinois, Nasser Syed

Dissertations

Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses not only corn, soybeans, …

Determining Bioindicators For Coastal Tidal Marsh Health Using The Food Web Of Larvae Of The Greenhead Horse Fly (Tabanus Nigrovittatus), Devika Rajeev Bhalerao

LSU Master's Theses

The greenhead horse fly Tabanus nigrovittatus Macquart is native to coastal marshlands from Texas to Nova Scotia. The larvae are apex invertebrate predators and their development is dependent on the food web in the soil. Surveillance of T. nigrovittatus after the 2010 Deepwater Horizon oil spill in the Gulf of Mexico showed population crashes of adults in the coastal marshes of East Louisiana near places where oil made landfall, but not in West Louisiana where the oil did not reach. Sediment collection in 2011 from West and East Louisiana revealed larval population crashes in the Eastern coastal region. We hypothesized …

K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler

Graduate Student Theses, Dissertations, & Professional Papers

Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …

Measuring The Human Gut Microbiome: New Tools And Non Alcoholic Fatty Liver Disease, Ruth G. Wong

Electronic Thesis and Dissertation Repository

With the advent of next generation DNA and RNA sequencing, scientists can obtain a more comprehensive snapshot of the bacterial communities on the human body (known as the `human microbiome'), leading to information about the bacterial composition, what genes are present, and what proteins are produced. The scientific community is in a phase of developing the experiments and accompanying statistical techniques to investigate the mechanisms by which the human microbiome affects health and disease. In this thesis, I explore alternatives to the standard weighted and unweighted UniFrac distance metric that measure the difference between microbiome samples. These alternative weightings allow …

A Case Study Tested Framework For Multivariate Analyses Of Microbiomes: Software For Microbial Community Comparisons, Eric M. Spaulding

Graduate Student Theses, Dissertations, & Professional Papers

The study of microbiomes is important because our understanding of microbial communities is providing insight into human health and many other areas of interest. Researchers often use genomic data to study microbial organisms, demonstrating differences from one organism to the next. Metagenomic data is utilized to study communities of microbial organisms. The research described herein involved the development of a collection of computational methods.

This suite of computational methods and tools (written in the R and Perl languages) has become a framework used for metagenomic data analysis and result visualization. Multivariate analyses such as Linear Discriminate Analysis (LDA) are used …

Developing Microbial Biomarkers To Non-Invasively Assess Health In Wild Elk (Cervus Canadensis) Populations, Samuel B. Pannoni

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to …

Optimal Clustering Techniques For Metagenomic Sequencing Data, Erik T. Cameron

Electronic Thesis and Dissertation Repository

Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering …

Functional Cloning And Characterization Of Antibiotic Resistance Genes From The Chicken Gut Microflora, Wei Zhou

Masters Theses

A recent study using human fecal samples in conjunction with a culture-independent approach revealed immense diversity of antibiotic resistance (AR) genes in the human gut microflora. We hypothesize that food animal gut microflora also contain diverse and novel AR genes which could contribute to the emergence and transmission of AR in pathogens important in animal and human health. To test this, we examined AR reservoir in chicken gut microflora using a metagenomic, functional cloning method. Total genomic DNA was extracted from individual cecal contents of two free range chickens and two conventionally raised chickens. The DNAs were physically sheered into …