Microbiology Commons^™

Bloom: A Microbial Self-Portrait, Emily Lauren Mulvaney

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Age-Associated Temporal Decline In Butyrate-Producing Bacteria Plays A Key Pathogenic Role In The Onset And Progression Of Neuropathology And Memory Deficits In 3×Tg-Ad Mice, Paula M Chilton, Smita S Ghare, Benjamin T Charpentier, Scott A Myers, Aakarsha V Rao, Joseph F Petrosino, Kristi L Hoffman, John C Greenwell, Neetu Tyagi, Jyotirmaya Behera, Yali Wang, Lucy J Sloan, Jingwen Zhang, Christopher B Shields, Gregory E Cooper, Leila Gobejishvili, Scott R Whittemore, Craig J Mcclain, Shirish S Barve

Faculty, Staff and Students Publications

Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis …

Scale And Habitat Effects On Measurement Of Streptomyces Biogeography And Biodiversity, Terilyn A. Stoflet

Cal Poly Humboldt theses and projects

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a …

Synergetic Signaling Between The Chlamydia Secreted Effectors Tarp And Tmea Regulates Actin Kinetics And Efficient Entry, Matthew Romero

Theses & Dissertations

Chlamydia trachomatis is both the leading cause of non-congenital preventable blindness in developing nations and the leading source of bacterial sexually transmitted infections. As an obligate intracellular pathogen, Chlamydia has an absolute requirement on gaining entry into its host, which is accomplished by manipulating the host actin cytoskeleton to assemble engulfment structures that drive pathogen entry. In support of this, Chlamydia secretes the effectors TarP and TmeA via a type-III secretion system, whose respective signaling outputs operate synergistically to generate rapid actin kinetics and efficient pathogen engulfment. Rapid actin recruitment characteristic of invading Chlamydia is derived from a collaborative interaction …

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …

A Retrospective, Observational Study Of 12 Cases Of Expanded-Access Customized Phage Therapy: Production, Characteristics, And Clinical Outcomes, Sabrina I Green, Justin R Clark, Haroldo H Santos, Kyle E Weesner, Keiko C Salazar, Saima Aslam, J William Campbell, Sarah B Doernberg, Emily Blodget, Michele I Morris, Gina A Suh, Karam Obeid, Fernanda P Silveira, Andrey A Filippov, Katrine L Whiteson, Barbara W Trautner, Austen L Terwilliger, Anthony Maresso

Faculty, Staff and Students Publications

BACKGROUND: Antimicrobial resistance (AMR) is undermining modern medicine, a problem compounded by bacterial adaptation to antibiotic pressures. Phages are viruses that infect bacteria. Their diversity and evolvability offer the prospect of their use as a therapeutic solution. Reported are outcomes of customized phage therapy for patients with difficult-to-treat antimicrobial resistant infections.

METHODS: We retrospectively assessed 12 cases of customized phage therapy from a phage production center. Phages were screened, purified, sequenced, characterized, and Food and Drug Administration-approved via the IND (investigational new drug) compassionate-care route. Outcomes were assessed as favorable or unfavorable by microbiologic and clinical standards. Infections were device-related …

Spatial Structure Formation By The Post-Transcriptional Gene Regulator Rsme In Pseudomonas Fluorescens Pf0-1, Anton Evans

Electronic Theses and Dissertations

Microorganisms are often found in microbial communities we call biofilms. Organisms living in these crowded environments have significant evolutionary pressure to retain access to the resources necessary to sustain life. My research uses the bacterium Pseudomonas fluorescens Pf0-1 to study how organisms evolve strategies to solve this crowding problem as aging colonies repeatedly generate mutant patches. These mutants expand the reach of the colony resulting in decreased local density as they push themselves up to the resource rich surface. These spatial structures result from social interactions between the mutant and the parental cells mediated through extracellular secretions, resulting in the …

Synthesis, Characterization And Antimicrobial Properties Of Mixed-Ligand Complexes Of Some Metal(Ii) Ions With Barbituric Acid And 1,10-Phenanthroline Ligands, Kayode Taiwo Ishola, Oluwabiyi James Olaoye, Mary Adelaide Oladipo, Omobola Ajibike Odedokun, Oyebanji Oluseun Aboyeji

Tanzania Journal of Science

Many pathogenic organisms have developed resistance to many antibiotics, which leads to an increase in the spread of many microbial infections. There is an urgent need to find more effective drugs to curb widespread transmission. Hence, this study synthesized and evaluated the antimicrobial activities of mixed-ligand complexes of Cu(II), Co(II), Ni(II), Mn(II), and Zn(II) ions with barbituric acid and 1,10 phenanthroline ligands in effort to find more effective antibiotics. The complexes were characterized using elemental analysis, metal analysis, melting points, solubility tests, and spectroscopic analyses (IR and UV-visible). The antimicrobial activities of the complexes were evaluated against two gram-positive bacteria …

Genomic And Proteomic Analysis Of An Erwinia Amylovora Phage, Alicia Brighton, Dr. Julianne Grose

Journal of Undergraduate Research

Fireblight is a disease, caused by the bacteria Erwinia amylovora, that can infect some fruit trees, including apple and pear trees. When an infection occurs, the effects can be devastating—any infected part of the tree must be removed and destroyed, sometimes resulting in loss of the entire tree. Furthermore, in the warm and moist conditions typical of springtime, the spread of fireblight can be nearly impossible to control with current management methods.¹

Characterization Of Lps As A Virulence Factor In Burkholderia Cepacia During Plant And Human Infection, Jack Klahr, Elizabeth Danka

Biology Senior Theses

Burkholderia cepacia is a gram-negative bacterium first characterized as the causative agent of sour skin in onion crops. More recently, B. cepacia has become a clinical concern as an opportunistic pathogen that can colonize the upper respiratory tract of cystic fibrosis patients and increase mortality in these patients. Infection is exacerbated by the intrinsic resistance to antibiotics found in this genus of organisms. Additional virulence factors help the bacteria persist in the host during infection. However, few of these factors have been described. In this work, we characterized a putative virulence factor that was first identified through an onion infection …

Detection And Capture Of Nitrogen Fixing Bacteria From Soil And Roots Using Plant Specific Lectins, Alana Horton

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Diazotrophs increase plant productivity by providing ammonia directly to plants in the rhizosphere or through association with the roots (Sun et al., 2021). Leveraging diazotrophs can aid in the reduction or application of harmful synthetic nitrogen fertilizers. This thesis aims to use plant root proteins, or lectins, to more rapidly recover viable diazotrophs that are likely to associate with crops. In this study, lectins, are used to recover bacteria from bulk soil by taking advantage of the binding relationship between lectins and bacterial cell surface polysaccharides. When commercially-available lectins were used with a magnetic pulldown to separate the lectin, bacterial …

Investigating The Effectiveness Of Microplastic Removal And The Relationship Between Microplastics, Bacterial Communities, And Nitrogen Cycling In The Natural Treatment Systems At The Arcata Wastewater Treatment Facility, Fiona Connor

Cal Poly Humboldt theses and projects

This thesis addressed two challenging aspects of microplastic research, including the quantification of microplastics in organic-rich water, and the investigation of how microplastics impact microorganisms and related nutrient-cycling. Two projects were designed and executed to address specific research objectives relating to these broad topics. The first objective was to develop and implement methods to determine the effectiveness of microplastic removal across the natural treatment systems at the Arcata Wastewater Treatment Facility (AWTF). The second objective was to observe how microplastics found in domestic wastewater impact the bacterial communities and nitrogen cycling in freshwater treatment wetland sediment through a bench-scale experiment, …

Comparing The Microbiomes Of Dental Plaques In 19th Century Ancestral Remains, Ananya Udyaver

Undergraduate Research Posters

During the construction of VCU’s Hermes A. Kontos Medical Sciences Building in April 1994, nineteenth century ancestral remains were found in an abandoned well on the Medical College of Virginia (MCV) campus. This well, now known as the East Marshall Street Well (EMSW), is thought to have been used as a disposal location for cadaver dissection for surgical and other medical waste in the past. VCU is now seeking to use DNA sequencing technology to match and assemble bones from each individual for a proper burial, uncover the cultural and historical context in which these people lived, and bring a …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Occurrence Of Kanamycin-Resistant Bacteria Relative To Anthropogenic Pollution Along Richland Creek In Nashville, Tn​, Jolene Ho Mach, Annie Le, Brandon Torres Ramirez

Science University Research Symposium (SURS)

The overuse of antibiotics has caused an increase in antibiotic-resistant (AR) bacteria, which is a serious public health concern. Previous studies showed a significant correlation between anthropogenic pollution and AR bacteria. This project aims to identify AR bacteria in Richland Creek relative to local anthropogenic pollution. Water samples were collected at four locations along Richland Creek in Nashville, Tennessee. Bacteria resistant to the antibiotic kanamycin were isolated from the water samples, identified to genera using DNA barcoding, and compared among the sites. We expect to see a greater abundance and diversity of kanamycin-resistant bacteria closer to the end than near …

Reproductive Ecology And Microbial Communities From Wood Duck Nest Boxes In Georgia And Florida, Jake Shurba

All Theses

Wood ducks (Aix sponsa) are an important game species throughout the Atlantic Flyway that was nearly extirpated by the early 20^th century due to overhunting and the loss of habitat. Wood ducks are secondary cavity-nesters that utilize artificial nest boxes and natural cavities. It is reported that the use of nest boxes is likely what led to re-establishment of the species in North America. Where boxes are numerous, overuse of boxes by multiple hens throughout a nesting season can occur and result in a buildup of bacteria, parasites and other potentially detrimental pathogens that can impact egg …

Effects Of Surface Topography On Macrophages And Bacterial Cells, Joseph Carnicelli

Theses - ALL

An association has been found between the texture of breast implants and anaplastic large cell lymphoma, which led to some textured implants to be withdrawn from the market in 2019. There is evidence that these cancers are associated with the harboring of bacteria on the surfaces of the textured implants. It is possible that specific topographic features hinder the removal of attached bacteria by inhibiting macrophage phagocytosis or promoting biofilm formation. Here we examine how bacteria and macrophages interact with recessive surface topographies as analogs to the surfaces seen on textured breast implants. Changes in bacteria morphology were observed among …

Dietary Fatty Acid Intake And The Colonic Gut Microbiota In Humans, Anthony A Xu, Luke K Kennedy, Kristi Hoffman, Donna L White, Fasiha Kanwal, Hashem B El-Serag, Joseph F Petrosino, Li Jiao

Faculty, Staff and Students Publications

A high-fat diet has been associated with systemic diseases in humans and alterations in gut microbiota in animal studies. However, the influence of dietary fatty acid intake on gut microbiota in humans has not been well studied. In this cross-sectional study, we examined the association between intake of total fatty acids (TFAs), saturated fatty acids (SFAs), trans fatty acids (TrFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), n3-FAs, and n6-FAs, and the community composition and structure of the adherent colonic gut microbiota. We obtained 97 colonic biopsies from 34 participants with endoscopically normal colons. Microbial DNA was used to …

An Investigation Of The Novel Use Of Bacteriophages To Diagnose And Treat Johne's Disease In Cattle, Max Kevane-Campbell

ORBioM (Open Research BioSciences Meeting)

Johne’s disease is a scourge to dairy farmers all over the world. It is an infectious disease that causes chronic inflammation and lesions along the inside of the small intestine of, primarily, ruminant animals (i.e., cattle and sheep). It is an incurable disease and urgently requires new and radical intervention strategies. Apart from careful on-site farm management practices, little can be offered to farmers to reduce the risk of infection, and nothing short of livestock culling is effective once an animal becomes infected. Currently, there are no vaccines licensed in Ireland or antibiotic treatment strategies available for Johne’s disease. This …

Temporal Changes In Gastrointestinal Fungi And The Risk Of Autoimmunity During Early Childhood: The Teddy Study, Thomas A Auchtung, Christopher J Stewart, Daniel P Smith, Eric W Triplett, Daniel Agardh, William A Hagopian, Anette G Ziegler, Marian J Rewers, Jin-Xiong She, Jorma Toppari, Åke Lernmark, Beena Akolkar, Jeffrey P Krischer, Kendra Vehik, Jennifer M Auchtung, Nadim J Ajami, Joseph F Petrosino

Faculty, Staff and Students Publications

Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over …

Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty

Undergraduate Research Symposium

Salmonella is a relatively abundant, virulent species of bacteria that is most known for spreading gastrointestinal diseases through food. These illnesses result in approximately 1.35 million infections, including over 25,000 hospitalizations each year, in the U.S. alone (CDC.gov). As antibiotic resistance becomes an increasingly urgent public health problem, the importance of developing alternative treatment methods is only becoming more crucial. One of the genes responsible for this virulence is known as hilA. HilA is the main transcriptional regulator of Salmonella Pathogenicity Island-1 gene (UniProt). SPI-1 plays an important role in the invasion of Salmonella into epithelial cells. The proteins encoded …

The Interaction Of Sulfate And Perchlorate And Its Implications On Bacterial Survival On Mars, Jack M. Richardson, Dylan Clark, Karly Kenny

2022 Symposium

Escherichia coli, Bacillus subtilis, and Staphylococcus aureus are all known spacecraft contaminants. This makes their viability to arrive and survive on Mars feasible, however, this could prove to be a great risk to the Martian environment. In order to test this possibility, all three species were grown within brines containing differing salts and salt concentrations. These salts and their corresponding concentrations are based on known data regarding Martian soil. Growth was measured over a course of 20 hours in solutions containing MgSO₄ at concentrations of 4.6% and 9.2%, Mg(ClO₄)₂ at concentrations of 0.6% and …

Assessing The Activity Of Antimicrobial Peptides Against Common Marine Bacteria Located In Rotifer (Brachionus Plicatilis) Cultures, Chelsea Woods, Lindsey Woolley, Gavin Partridge, Mengqi Chen, Evan F. Haney, Robert E.W. Hancock, Nicky Buller, Andrew Currie

Fisheries Research Articles

Rotifers are used as the first feed for marine fish larvae and are grown in large cultures that have high loads of organic matter and heterotrophic bacteria; these bacteria are passed on to the developing fish larvae and can potentially lead to bacterial infections. A modified minimum inhibitory concentration (MIC) protocol for antimicrobial peptides was used to determine the potency of ten antimicrobial peptides (AMPs) in artificial seawater relevant to a rotifer culture (salinity of 25‰) against common marine pathogens. All of the AMPs had antimicrobial activity against the bacterial isolates when the salt concentration was approximately zero. However, in …

Antibiotic-Resistant Bacteria In Freshwater Crayfish, Colby Finch

Honors Theses

The presence of antibiotic-resistant bacteria is increasing in natural aquatic environments. Alongside this, organisms that live in these ecosystems are increasingly harboring antibiotic-resistant bacteria. In this study, I analyzed the capacity for the crayfish species Procambarus vioscai paynei to harbor antibiotic-resistant bacteria. Crayfish, as well as water and sediment, were sampled from a pond at the University of Mississippi Field Station. The guts of crayfish were plated on TSA agar, as well as agar containing vancomycin, erythromycin, penicillin, tetracycline, or ciprofloxacin. Following incubation, counts of bacteria were determined. Selected bacterial isolates were tested for multiple antibiotic-resistance. Bacterial isolates were also …

Identification Of Critical Points For Bacterial Contamination In The Microbrewery Environment, Alex Ryan Thompson

All Theses

There are 8,884 craft breweries producing over 23 million barrels of beer in the United States as of 2020. These 23 million barrels of craft beer account for 12.3% of the United States beer consumption in 2020. The American craft beer industry is substantial and needs to protect its product from bacterial contamination.

Overall, beer is a microbially stable product. Beers pH, ethanol levels, CO₂ concentrations, the presence of hop-derived antimicrobial compounds, and low levels of O₂ make beer a highly unfavorable environment for most bacterial species. Furthermore, the brewing process, which involves heat treatments and chemical sanitizers …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Pre-Exposure Of Escherichia Coli And Staphylococcus Aureus To Sub-Bactericidal Concentrations Of Benzalkonium Chloride And Its Effect On Low-Level Antimicrobial Resistance, Logan Fette

All Graduate Theses, Dissertations, and Other Capstone Projects

Antimicrobial resistance that develops in bacteria is a highly studied aspect of microbiology due to the concerns that it poses for public health. Antibiotics remain our primary care option when dealing with bacterial infections. The concept of tolerance of bacteria to disinfectants is similar and it also poses a significant health risk. Since use of disinfectants for sanitation is a primary manner in which we are able to prevent potential infections from occurring in the first place, it can be a helpful means to preventing development of antimicrobial resistance. However, what has not been explored to the same extent is …

Biodegradation Of Rubber Particles In Soil: Using Acclimated Bacteria Isolated From Kansas Soil To Degrade Cryogrinds In Slurry, Shane Graham

Williams Honors College, Honors Research Projects

This study investigated the viability of bioremediating rubber cryogrind using enriched indigenous bacteria. To begin the experiment, soils from three highway roadside locations in Kansas, KS 96 and West, KS 400 and 143^rd, and 199^th, were collected and transported to the lab to be studied. An initial soil characterization was run on the soil samples using distilled (DI) water mixture and 0.01 M CaCl₂ to assess conductivity. The soils were tested to gather a baseline of the relationship between pH and conductivity and the impact of its distance from the roadside. Bacteria were isolated from …

Interleukin-1Β Secretion Induced By Mucosa-Associated Gut Commensal Bacteria Promotes Intestinal Barrier Repair, Wan-Jung H Wu, Myunghoo Kim, Lin-Chun Chang, Adrien Assie, Fatima B Saldana-Morales, Daniel F Zegarra-Ruiz, Kendra Norwood, Buck S Samuel, Gretchen E Diehl

Faculty, Staff and Students Publications

The gut microbiota is essential for maintenance and repair of the intestinal epithelial barrier. As shifts in both intestinal epithelial barrier function and microbiota composition are found in inflammatory bowel disease patients, it is critical to understand the role of distinct bacteria in regulating barrier repair. We identified a mouse commensal E. coli isolate, GDAR2-2, that protects mice from Citrobacter rodentium infection and dextran sulfate sodium-induced colitis. Colonization with GDAR2-2 in mice resulted in expansion of CX3CR1+ mononuclear phagocytes, including CX3CR1+ macrophages/dendritic cells and monocytes, along with IL-22-secreting type 3 innate lymphoid cells and improved epithelial barrier function. In vitro …