Life Sciences Commons^™

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Acinetobacter Baumannii - The Perfect Pathogen, Jesse Guzik, Myrna Rezcallah, Alexcia Zeller, Kaite Mattson

Research and Scholarship Symposium Posters

Acinetobacter was discovered in 1911 by Martinus Beijerinck. Acinetobacter baumannii didn't receive its scientific name until 1986. A. baumannii is now commonly referred to as "Iraqibacter" due to a rise in infections among US military personnel returning from Iraq and Afghanistan. After the Iraq War began in 2003, the frequency of cases began to rise, especially among patients in intensive care units. Patients using ventilators, catheters, have postoperative wounds, stay in the hospital for an extended period of time, or are immunocompromised are at a considerably higher risk of getting A. baumannii. Because of its large number of virulence …

Complete Genome Sequences Of Chop, Delrio, And Grandslam, Three Gordonia Phages Isolated From Soil In Central Arkansas, Heidi N. Mathes, Elijah I. Christenson, John H. Crum, Emme M. Edmondson, Kassidy E. Gray, Luke W. Lawson, Lauren E. Lee, Michael P. Lee, Jackson A. Lipscomb, Morgan E. Masengale, Hannah G. Matthews, Charles M. Mcclain 4th, Tuesday N. Melton, Trace H. Morrow, Alexis M. Perry, David R. Rainwater, Grace E. Renois, Maryann F. Rettig, Duncan C. Troup, Allie J. Wilson, Nathan Reyna, Ruth Plymale

Articles

Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.

Diverse Marine T4-Like Cyanophage Communities Are Primarily Comprised Of Low-Abundance Species Including Species With Distinct Seasonal, Persistent, Occasional, Or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, Nathan A. Ahlgren

Biology

Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.

Structural Analysis Of Predicted Proteins Using Alphafold, Brydon P. Wall

Undergraduate Research Posters

The function of around 67% of predicted proteins from genes in Mycobacteriophage CheetoDust can not be confidently predicted using traditional techniques and can only be functionally labeled “hypothetical proteins”. However, a new approach using AlphaFold, an artificial intelligence tool to generate a structural prediction from a sequence, can take advantage of structurally conserved regions that were previously obfuscated to gain new insights and visualize data in new ways.

Since amino acid sequences are more conserved than its corresponding DNA sequence, amino acid sequences are used when predicting the function of the corresponding translated protein. Until recently, predicting structure from an …

Characterization Of A Stenotrophomonas Maltophilia Bacteriophage, Edward Eshoo

College of Science and Health Theses and Dissertations

Stenotrophomonas maltophilia is a ubiquitous Gram-negative, multidrug resistant, opportunistic bacterial pathogen that causes various infections in humans. Recently, the use of bacteriophages as therapeutic agents, has gained interest as an alternative to traditional antibiotics. This thesis describes the isolation, purification, and characterization of S. maltophilia bacteriophage Bfi2 and discusses its activity against related, and often co-isolated, bacterial pathogens. Amplification of the phage resulted in clear, well-defined plaques and a titer of 1.73 ± 0.38 x 1011 PFU/ml. Bfi2 demonstrated the ability to lyse 55% of the S. maltophilia strains tested, suggesting that it has a moderate host range. However, the …

Implications Of Antibiotic And Bacteriophage Resistance In Environmentally Isolated E. Coli, Michael Connolly

Honors Theses

The increasing prevalence of antibiotic-resistant bacteria is an emerging problem for humans. Clinical misuse, overuse in agricultural and food settings, and limited numbers of new antibiotics have accelerated the proliferation of antibiotic-resistant bacteria. To confront this threat, scientists must develop new therapeutics that kill these antibiotic-resistant bacteria. In this study, we used Escherichia coli to analyze antibiotic and bacteriophage susceptibility. E. coli is a common, mostly benign, enteric, gram-negative bacteria. We isolated three E. coli strains from the Hans Groot Kill, a stream that runs through Union College’s campus. We sought to assess various E. coli strains’ antibiotic resistance, susceptibility …

Aeromonas Phage Research And The Public Health Impact Of Antibiotics In Aquaculture Workers, Madelyn Merchant

Honors Projects

One of the most common fish diseases in aquaculture is Aeromonas infection. The most common way to treat this infection is through antibiotics. The bacteria in the fish can become antibiotic-resistant and perpetuate the disease. The diseases in fish create a huge financial loss and the industry loses $6 billion per year due to diseases in fish. An alternative to antibiotics is bacteriophage which causes less environmental degradation and is better for human gut flora. In aquaculture there have been examples of aquaculture workers becoming sick from the water in aquaculture ponds as well as from people eating the fish. …

Elucidation Of Novel And Established Campylobacter Species With Clinical And Agricultural Significance Through Phenotypic, Genotypic, And Taxonomic Investigation, Caoimhe Lynch

Theses

Campylobacter spp. are well-established human, veterinary and economic pathogens, with a broad host range spanning from terrestrial and marine mammalian, avian and reptilian hosts. The scope of the study includes novel and notorious species within the genus, with reference to zoonotic agents Campylobacter jejuni and Campylobacter coli - the leading cause of human bacterial gastroenteritis in the EU and Ireland, Campylobacter fetus that represents the most common campylobacter causing bacteraemia and two novel species isolated from pigs not described in the literature previously. C. jejuni and C. coli isolates (n = 350) recovered from broiler caecal and neck skin samples, …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

Evolution And Selection: From Suppression Of Metabolic Deficiencies To Bacteriophage Host Range And Resistance, Daniel Kurt Arens

Theses and Dissertations

The evolution and adaptation of microorganisms is so rapid it can be seen in the time frame of days. The root cause for their evolution comes from selective environmental pressures that see organisms with beneficial mutations survive otherwise deadly encounters or outperform members of its population who fail to adapt. This does not always result in strict improvement of the individual as in the case of antibiotic resistant bacteria who often display fitness tradeoffs to avoid death (see Reviews [1-3]). For example, when an ampicillin resistance gene (ampC) containing plasmid that is occasionally found in the wild was transformed into …

Innovative Approaches In The Discovery Of Aquatic Mycobacteriophages, Janis H. Doss

Biomedical Sciences Theses & Dissertations

Bacteriophages (phages), viruses that infect bacteria, have many applications in medicine, agriculture, molecular biology, and other fields. As antibiotic resistance becomes an increasing problem, interest in phages has grown. The traditional techniques of phage discovery are successful for some phages, but others require modified procedures to achieve detectable host infection.

Mycobacterium is a diverse bacterial genus characterized by a unique cell wall containing mycolic acids, which aids in survival and pathogenesis. The aims of the present research were to isolate mycobacteriophages, use bioinformatics techniques to analyze mycobacterial prophages, and combine genetic analysis with multi-well plate host range studies to identify …

Isolation And Characterization Of Pectobacterium Phage Vb_Patm_Cb7: New Insights Into The Genus Certrevirus, Colin Buttimer, Caoimhe Lynch, Hanne Hendrix, Horst Neve, Jean Paul Noben, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the …

Lysogeny And Use Of Mycobacteriophage Pita2, Eleanor Behling, Neocles B. Leontis, Jill Zeilstra-Ryalls

Honors Projects

The CDC has classified antibiotic resistance as the biggest health challenge of our era; every year 2 million lives are impacted and even lost due to resistant bacteria. Bacteriophages provide an alternative route to fighting infections that does not further the development of antibiotic resistance among bacterial species. A bacteriophage replicates inside a bacterial cell and then causes that cell to lyse, an event that kills the bacterial host. However, some phage can integrate their genomes into the host chromosome without causing lysis. The HHMI SEA-PHAGES program has generated a collection of bacteriophage that infect Actinobacteria species. Over 13,000 phages …

Prokaryotic And Viral Community Composition Of Freshwater Springs In Florida, Usa, Kema Malki, Natalie A. Sawaya, Anna J. Székely, Michael J. Tisza, Mya Breitbart

Marine Science Faculty Publications

Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 10³ ml⁻¹ to 1.1 × 10⁵ ml⁻¹ and 2.2 × 10³ ml …

Bioinformatics Identification Of Anti-Crispr Loci By Using Homology, Guilt-By-Association, And Crispr Self-Targeting Spacer Approaches, Yanbin Yin, Bowen Yang, Sarah Entwistle

Department of Food Science and Technology: Faculty Publications

Anti-CRISPR (Acr) loci/operons encode Acr proteins and Acr-associated (Aca) proteins. Forty-five Acr families have been experimentally characterized inhibiting seven subtypes of CRISPR-Cas systems. We have developed a bioinformatics pipeline to identify genomic loci containing Acr homologs and/or Aca homologs by combining three computational approaches: homology, guilt-by-association, and self-targeting spacers. Homology search found thousands of Acr homologs in bacterial and viral genomes, but most are homologous to AcrIIA7 and AcrIIA9. Investigating the gene neighborhood of these Acr homologs revealed that only a small percentage (23.0% in bacteria and 8.2% in viruses) of them have neighboring Aca homologs and thus form Acr-Aca …

Isolation, Genetic Characterization And Clinical Application Of Bacteriophages Of Pathogenic Bacterial Species, Trever Leon Thurgood

Theses and Dissertations

Bacteriophages (phages) are the smallest biological entity on the planet. They provide vast amounts of valuable knowledge to biologists. Phage genomes are relatively simple compared to the organisms they infect (prokaryotes) and yet continually point to the complexity surrounding molecular- and microbiological mechanisms of life. By studying phages we can learn of the systems of gene expression, protein interaction and DNA organization. Phages are useful not only from an academic perspective, but may also have useful clinical applications. In the face of the rise of antibiotic-resistant bacterial “super pathogens”, scientists and researchers turn to phages as alternative treatments to these …

Microscopic Saviors: The Use Of Phages In Medicine, Roger Sherman

D.U.Quark

The influenza virus has plagued humans for centuries. Recently antiviral medications, which shorten the duration of the flu, have been introduced into society. These medications along with vaccinations, which try to give the body immunity before the virus strikes, help to stop the flu before it attacks the host. The virus, however, replicates using host cells and can slightly change itself with each replication, which over time could lead to a strain immune to the current antiviral medication and vaccines. However, using more preventative measures could help slow the changing strains of the flu virus. Using vaccines to stop the …

Further Understanding Of Bacteriophages That Infect The Bacterial Family Enterobacteriaceae, Paul Flake

Undergraduate Honors Theses

Despite the eclectic nature of bacteriophage genomes, nucleotide comparison is an effective method for grouping phages into cluster and subcluster classifications. This process is facilitated by making preliminary cluster assignations based on the identity of the major capsid protein. As more phages continue to be sequenced and integrated into cluster/subcluster groupings, adjustments may need to be made to the genomic similarity percentages that have previously defined cluster/subcluster classifications. Implementing proteomic comparison in addition to nucleotide homology may provide added clarity to this process. Protein conservation and diversity among lytic phages that infect the bacterial family Enterobacteriaceae is discussed and the …

Comparison Of Bacteriophage Annotation Methods, Alicia Salisbury, Philippos Tsourkas

McNair Poster Presentations

The rise of antibiotic-resistant bacteria has increased interest in bacteriophages (viruses that kill bacteria) in recent years. Due to the decreasing cost of genome sequencing, the number of sequenced phage genomes is growing at a geometric rate. Sequencing is followed by annotation, in which genes, start codons, and putative protein functions are identified. Most phage genomes are auto-annotated with programs designed for prokaryotes. Accuracy metrics for these programs with regard to phage genomes are not available. The genome of Escherichia coli phage Lambda was used to benchmark the accuracy of several genome annotation methods and programs. Discovered in 1951, Lambda …

Pectobacterium Atrosepticum Phage Vb_Patp_Cb5: A Member Of The Proposed Genus ‘Phimunavirus’, Colin Buttimer, Alan Lucid, Horst Neve, Charles M.A.P. Franz, Jim O’Mahony, Dann Turner, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages 'M1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct …

Bacteriophages As Beneficial Regulators Of The Mammalian Microbiome, Joseph W. Francis, Matthew Ingle, Todd Charles Wood

Proceedings of the International Conference on Creationism

Much of the research on viruses has concentrated on their disease causing ability. The creation model biomatrix theory predicts that viruses play a beneficial role in cells and organisms. In this report we present a new theory which proposes that mammalian phages (bacteriophages), the most abundant organism associated with mammals, guard and regulate growth of the mammalian microbiome. We base this theory on nearly a century of published evidence that demonstrates that phage can insert into the bacterial genome and cover the surface of bacteria. We propose that this “cloaking” of the bacterial cell surface is an elegant mechanism whereby …

Isolation Of Stenotrophomonas Maltophilia Virus Bfi1: A Biofilm Inhibiting Phage, Thomas Edward Moran

College of Science and Health Theses and Dissertations

The bacterium Stenotrophomonas maltophilia is an emerging infectious pathogen of global concern. Due to its drug-resistant nature, there are limited treatment options available. A potential option for combating S. maltophilia infections is phage therapy, the medicinal use of viruses to treat bacterial infections. Stenotrophomonas phage Bfi1 was isolated from a soil sample using S. maltophilia clinical strain S18202. Transmission electron microscopy provided evidence that this phage is a member of the Siphoviridae family. Host range analysis showed that the phage successfully infected and lysed 30% of the S. maltophilia strains tested. Genomic analysis revealed that the phage contains approximately 32.2-56.5 …

Unprecedented Diversity Of Ssdna Phages From The Family Microviridae Detected Within The Gut Of A Protochordate Model Organism (Ciona Robusta), Alexandria Creasy, Karyna Rosario, Brittany A. Leigh

Marine Science Faculty Publications

Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system …

Unprecedented Diversity Of Ssdna Phages From The Family Microviridae Detected Within The Gut Of A Protochordate Model Organism (Ciona Robusta), Alexandria Creasy, Karyna Rosario, Brittany Leigh, Larry Dishaw, Mya Breitbart

Marine Science Faculty Publications

Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system …

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Catherine Putonti

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut

Undergraduate Research Symposium Posters

A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program …

Combating Obesity Through Gut Microbiome Targeted Bacteriophage Therapy, Jeffrey Gongze Zhao, Laura C. Bridgewater

Library/Life Sciences Undergraduate Poster Competition 2017

Obesity has become a serious health issue in the world (Ogden 2012), and its correlation to the human gut microbiota has been studied extensively since 2007 (Cani 2007). In 2013, researchers identified Enterobacter cloacae B29 from an obese patient’s gut and demonstrated its causal relationship to the host’s obese symptoms( Fei & Zhao 2013). However, there have not been many methods developed to alleviate obesity symptoms through eliminating pathogenic endotoxin-producing bacteria (such as E. cloacae B29), from the host’s gut flora. In this research, I propose a new strategy for treating obesity by using gut microbiome targeted bacteriophage therapy. …

The Role Of Phage Trnas In The Evolution Of Codon Usage Biases In Giant Pseudomonas Phage Phikz And El, Stephanie Steidel

Master's Theses

As the most abundant and diverse biological agents in the biosphere phage have significant roles in microbial ecology, acting both as lethal bacterial parasites and vehicles of horizontal gene transfer. Phage/host coevolution drives optimization of phage codon usage for use of host translational machinery, thus lowered correspondence between phage and host codon usage reduces viral fitness. Some phage may partially bypass host translational selection on their codon usage by encoding their own tRNAs, although the effects of these tRNAs on phage codon usage and translation has not been well examined. This work explores the influence of phage encoded tRNAs on …

Isolation Of A Novel Phage Otoolekemple52, Thomas O. Raymond

Undergraduate Research Posters

A bacteriophage is a virus capable of infecting bacteria like ubiquitous soil-dwelling genus Bacillus. Within the Bacillus genus, there is the “ACT family” made up of B. thuringiensis, B. cereus, and B. anthracis, which are highly related but with different pathogenic characteristics. Because of this, phages isolated using a species in this group may have a broad host range encompassing several species from Bacillus. Since B. cereus and B. anthracis can result in fatal to mild sickness in humans, the non-pahtogenic B. thuringiensis kurstaki was used to discover and characterize novel phages. The phage OTooleKemple52 was isolated …