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Articles 1 - 15 of 15
Full-Text Articles in Other Microbiology
Integration Of Multi-Omics Datasets Evaluating Structural And Functional Features Of The Gut Microbiome In People With Hiv (Pwh)., Aakarsha Vijayakumar Rao
Integration Of Multi-Omics Datasets Evaluating Structural And Functional Features Of The Gut Microbiome In People With Hiv (Pwh)., Aakarsha Vijayakumar Rao
Electronic Theses and Dissertations
Gut dysbiosis characterized by reduced abundance of beneficial butyrate-producing bacteria has been independently linked to HIV-1 infection and heavy alcohol drinking. Further, gut dysbiosis results in loss of gut barrier integrity, microbial translocation and host-specific systemic inflammation. Therefore, to evaluate the functional consequences of structural changes in the gut microbiome, integrated data analysis is imperative. In this dissertation, we perform integrated analyses using data from multi-omics platforms to examine the structural and functional features of the gut microbiome of PWH. Gut microbiome composition was evaluated by sequencing V4 region of 16S rDNA, concentrations of metabolites and host-specific immune markers were …
Expression, Characterization, And Comparative Analysis Of Bacillus Bacteriophage Endolysins, Stephen D. Zdgiebloski
Expression, Characterization, And Comparative Analysis Of Bacillus Bacteriophage Endolysins, Stephen D. Zdgiebloski
Research and Creativity Symposium
Bacteriophages present a promising alternative for combating antibiotic-resistant bacteria without disrupting the normal microbiome or harming human cells. The antibacterial properties of lytic bacteriophages are largely attributed to endolysins, enzymes active in the lytic cycle. Endolysins recognize bacterial cell walls and cleave the peptidoglycan matrix, leading to cell wall disruption. Their specificity and effectiveness against bacterial hosts are determined by two functional domains, including the cell wall binding domain. Our research focuses on characterizing Bacillus phage endolysins. We analyzed the protein sequences of endolysins from six Bacillus phages isolated at the University of Mary Washington. Although these phages were isolated …
Establishment Of Bacteroides In The Gut And Its Role In The Cystic Fibrosis Gut-Lung Axis, Rebecca A. Valls
Establishment Of Bacteroides In The Gut And Its Role In The Cystic Fibrosis Gut-Lung Axis, Rebecca A. Valls
Dartmouth College Ph.D Dissertations
In the quest to understand the complex interplay between the gut microbiota and cystic fibrosis (CF), a disease characterized by chronic upper respiratory complications and an exacerbated proinflammatory response, our lab engaged in a collaborative study with Dartmouth-Hitchcock Medical Center (DHMC) to characterize the gut microbiota of pediatric CF patients. Initial analyses established a connection between gut microbial composition and respiratory health, particularly highlighting a scarcity of Bacteroides species compared to healthy controls. In following investigations, we utilized random forest models to understand how stool microbiota may influence clinical outcomes of these pediatric CF patients, including: age, upper respiratory infections, …
Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik
Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik
Master's Theses
Blueberries are an important agricultural commodity in all over the United States. Due to its health benefits, there is a huge demand globally, thus expanding the industry. Breeding programs are essential to maintain such industries. Challenges that play a role in contemporary breeding programs are various biotic and abiotic stress factors. Studies have shown that microorganisms are recruited by plants to alleviate them during stressful conditions. Though blueberries have been cultivated for about 100 years, how the microbiome has been affected due to this is poorly understood. We hypothesized that interspecific crosses and artificial selection have significantly changed the microbiome …
Metagenome-Wide Associations And Metabolic Modeling To Predict The Biomarkers For Colorectal Cancer, Nagavardhini Avuthu
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 …
Evolution And Clinical Relevance Of Vaginal Bifidobacterium Breve In The Vaginal Environment, Nicole R. Jimenez
Evolution And Clinical Relevance Of Vaginal Bifidobacterium Breve In The Vaginal Environment, Nicole R. Jimenez
Theses and Dissertations
The vaginal microbiome is important in reproductive health and disease and is often dominated by lactobacilli. However, there are many other community state types dominated by single species that are still not well characterized. Bifidobacterium species such as Bifidobacterium breve and Bifidobacterium longum have been observed to dominate vaginal profiles. Bifidobacteria are important in infant gut development, but little is known about their role in vaginal health. Thus, we sought to use a multisystem approach to better characterize Bifidobacterium species present in the vaginal microbiome with an emphasis on B. breve. Eight strains of B. breve were isolated from vaginal …
Effect Of Zinc On Microcystis Aeruginosa And Its Toxin Production, Jose L. Perez
Effect Of Zinc On Microcystis Aeruginosa And Its Toxin Production, Jose L. Perez
Seton Hall University Dissertations and Theses (ETDs)
Cyanobacteria harmful algal blooms (CHABs) are globally increasing biomasses of detrimental cyanobacteria due to anthropogenic water phosphorous and nitrogen loading and climate change. CHABs often produce secondary metabolites, cyanotoxins, that cause harmful effects to organisms, most water systems, and socioeconomic infrastructures. Additionally, the presence of heavy metal pollutant runoff in CHAB affected environments may result in CHAB population changes – aggravating toxigenicity. Zinc metal resistance and stress response were studied in microcystin (MC) cyanotoxin-producing Microcystis aeruginosa UTEX LB 2385 (M. aeruginosa UTEX LB 2385) and non-MC producing Microcystis aeruginosa UTEX LB 2386 (M. aeruginosa UTEX LB 2386) cyanobacteria. Molecular analysis …
The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi
The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi
Dissertations
Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …
Characterization Of Bacterial Isolates Obtained From Commercial Poultry Feed And Retail Food Using Whole Genome Sequence Analysis And Selected Biochemical Tests, Elena George Olson
Characterization Of Bacterial Isolates Obtained From Commercial Poultry Feed And Retail Food Using Whole Genome Sequence Analysis And Selected Biochemical Tests, Elena George Olson
Electronic Theses & Dissertations
The goals of this study is two-fold. The first part investigates bacterial isolates from commercial poultry feed and the second part deals with bacterial isolates recovered from retail food. In order to reduce pathogen contamination in poultry products identification of overall microbial populations in poultry production processing steps have always been considered an important monitoring tool for assessing sanitizer effectiveness and the corresponding responses of bacteria load levels on poultry carcasses. Bacterial isolates recovered from corn-based chicken feed were purified on aerobic plate count agar and eleven morphologically different colonies were selected for whole genome sequencing. In this part, the …
An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao
Chemistry and Chemical Biology ETDs
Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these …
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest
Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest
Interdisciplinary Research Data
To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381
Identification, Characterization, And Life Cycle Of Intein-Associated Homing Endonucleases, Joshua J. Skydel
Identification, Characterization, And Life Cycle Of Intein-Associated Homing Endonucleases, Joshua J. Skydel
Honors Scholar Theses
Inteins are molecular parasites that have been identified in unicellular organisms from the three domains of life. The intein self-excises following translation of the host gene, and therefore incurs a fitness cost for its carrier. The symbiotic state of the intein to its host is dependent on the presence or absence of a homing endonuclease domain, which facilitates horizontal transfer of the molecule. Identification of this domain provides information on the evolutionary history of the intein, as well as patterns of horizontal gene transfer in microbial communities. I have therefore developed Hidden Markov Models (HMMs) to identify homing endonuclease domains …
Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield
Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield
Theses and Dissertations
The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …
A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe
A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe
Department of Biological Sciences Publications
The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …
Prokaryotic Diversity In The Rhizosphere Of Organic, Intensive, And Transitional Coffee Farms In Brazil, Adam Caldwell, Livia Silva, Cynthia Da Silva, Cleber Ouverney
Prokaryotic Diversity In The Rhizosphere Of Organic, Intensive, And Transitional Coffee Farms In Brazil, Adam Caldwell, Livia Silva, Cynthia Da Silva, Cleber Ouverney
Faculty Publications, Biological Sciences
Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 …