Microbiology Commons^™

Variable Fire Behavior Causes Greater Bacterial And Fungal Richness, James A. Lutz, Joseph D. Birch

Wildland Resources Faculty Publications

Results of research in forest health and forest futures in Utah.

Key Results

1. Fire reduces microbial richness

Nine years after fire, burned soils had 19 - 31% lower richness, compared to unburned refugia.

2. Pathogens like it hot?

Pathogens made up a larger proportion of burned communities compared to unburned refugia.

3. Unburned refugia communities are tough

Refugia communities had greater resistance to disturbance than burned communities.

Antibiotic Resistance Profile Of Enterobacteriaceae Isolated From Healthy Pigs In The Republic Of Armenia, Yura Shirvanyan, Irma Artushyan, Lilit Hovsepyan, Ashkhen Shirvanyan, Elmira Ghazaryan, Tigran Markosyan

The Thai Journal of Veterinary Medicine

The rising prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae in livestock presents a significant threat to both animal and human health. This study investigates the antibiotic resistance profiles of Enterobacteriaceae isolated from 160 samples collected from the lymph nodes of healthy pigs in Armenia. Fifty isolates were identified, including Escherichia coli (24), Klebsiella spp. (10), Salmonella spp. (6), Raoultella ornithinolytica (4), Pseudomonas aeruginosa (4), and Proteus mirabilis (2). Resistance was evaluated using the disk diffusion method against 22 antibiotics from nine classes. Alarmingly, 94.5% of isolates were resistant to clarithromycin and 90.3% to erythromycin, while resistance to cephalothin and amoxicillin …

Cyanobacteria And Algae From Chýnov And Koněprusy Caves (Czech Republic), Michaela Wipplingerová, Jan Pokorný, Jan Kaštovský

International Journal of Speleology

Algae and cyanobacteria have been studied in two so far phycologically unexplored show caves (Chýnov and Koněprusy) in the Czech Republic. Taxa were identified morphologically using cultivation and subsequent light microscopy, while problematic cyanobacterial species were verified by sequencing the genes for 16S rRNA and 16S–23S internal transcribed spacer. A total of 13 cyanobacterial taxa were found, two Bacillariophyceae, three Xanthophyceae, four Chlorophyceae, six Trebouxiophyceae, 11 Streptophyta, and three Euglenida; many of these species were found for the first time in the caves. The darker parts of the caves were dominated by cyanobacteria, and green algae were found predominantly right …

Prodrug Activation In Malaria Parasites Mediated By An Imported Erythrocyte Esterase, Acylpeptide Hydrolase (Apeh), Sesh A. Sundararaman, Justin J. Miller, Ellora C. Daley, Kelsey A. O'Brien, Paulina Kasak, Abigail M. Daniels, Rachel L. Edwards, Kenneth M. Heidel, Darean A. Bague, Madeleine A. Wilson, Andrew J. Koelper, Elexi C. Kourtoglou, Alex D. White, Sloan A. August, Georgia A. Apple, Regis W. Rouamba, Anthony J. Durand, John J. Esteb, Florian L. Muller, R. Jeremy Johnson, Geoffrey C. Hoops, Cynthia S. Dowd, Audrey R. Odom John

College of Health Professions Faculty Papers

The continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by undesirable drug-like properties of lead compounds. Prodrug approaches temporarily mask undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin (Fsm), exhibit significantly higher antimalarial potency than their parent compounds [R.L. Edwards et al., Sci. Rep. 7, 8400 (2017)]. However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH), is the major activating enzyme of multiple …

Confounding Factors Of Cervical Carcinogenesis And Cervical Cancer Health Disparity, Vivek Kumar Kashyap, Namita Sinha, Nadeem Zafar, Murali M. Yallapu, Santosh Kumar, Everardo Cobos, Subhash C. Chauhan

Research Symposium

Clinical studies show that cervical cancer is the most frequently detected cancer in women living with human immunodeficiency virus (HIV), which has been defined as an acquired immunodeficiency syndrome (AIDS). Women living with HIV are 6 times more likely to develop cervical cancer compared to the general population, and an estimated 5% of all cervical cancer cases are attributable to HIV. Studies suggest that several genes are involved in different molecular pathways, which can influence the vulnerability, severity, or advancement of cervical cancer in the presence of HIV and human papillomavirus (HPV) co-infection. Clinical studies have also shown levels of …

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Screening For Penicillin G Acylase (Pga)-Producing Bacteria And Gene Cloning Using Degenerate Oligonucleotide Primed-Pcr, Masdalifah Masdalifah, Sri Rezeki Wulandari, Gabriela Christy Sabbathini, Maria Ulfah, Dini Achnafani, Ahmad Wibisana, Feronika Heppy Sriherfyna, Is Helianti, Niknik Nurhayati

Makara Journal of Science

The growing concern over antibiotic resistance has driven global efforts to explore innovative solutions, including the use of Penicillin G acylase (PGA) to produce semisynthetic β-lactam antibiotics. This study screened four potential in-tracellular PGA-producing bacteria: Alcaligenes faecalis InaCC B444 (AfPGA), Kluyvera cryocrescens InaCC B850 (KcPGA), Providencia rettgeri InaCC B25 (Pr25PGA), and P. rettgeri InaCC B466 (Pr466PGA). Penicillin G Acylase encoding genes (pgas) were isolated from them using a Degenerate Oligonucleotide Primed-PCR (DOP-PCR) approach and sequenced. Microbiological assays confirmed all tested crude extracts to exhibit inhibitory effects. Penicillin G was used for evaluating hydrolytic activity and 6-Amino Penicillanic Acid (6-APA) coupled …

Antibacterial Activity Of Endophytic Actinobacteria Isolated From Ziziphus Mauritiana Against Multidrug-Resistant Strains, Hafifatunil Khairani, Jepri Agung Priyanto, Muhammad Eka Prastya, Dwi Retnowati

Makara Journal of Science

Increasing resistance to existing antibiotics has led to a need for new alternative sources. Among the possibilities that need to be explored is the endophytic actinobacteria associated with Ziziphus mauritiana. The present study aimed to evaluate the antibacterial activity of endophytic actinobacteria isolated from Z. mauritiana against five multidrug-resistant bacterial strains. Thirty actinobacteria isolates were obtained from the roots, stem, and leaves of the plant using the serial dilution technique. Using a double-layer agar test, we found that colonies from five of the 30 isolates (16%) exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and the M18 strain of Bacillus …

Virulence Analysis, Characterization Of Integron, And Antimicrobial Resistance Genes In Strains Of Acinetobacter Baumannii Recovered From The Hydrological Sub-Region Of Soto La Marina, Tamaulipas, Tunde Olarinde Olaniyan, Ana Verónica Martínez Vázquez, Susana Silvia Fernández Dávila, Cesar Marcial Escobedo Bonilla, Virgilio Bocanegra Garcia

Research Symposium

Background: Acinetobacter baumannii (A. baumannii) is an important bacterium due to its frequent recovery as a multidrug-resistant pathogen in hospital settings. Its antimicrobial resistance capacities made it an important challenge to health care. Colistin has been adopted as the last resort drug for managing infections associated with A. baumannii and many other multidrug-resistant Gram-negative bacteria (MDR-GNB). Because of the rise in the use of colistin for the treatment of MDR-GNB, the evolution and spread of colistin-resistant bacteria is possible thus raising a potential threat to public health. However, we have chosen to focus on A. baumannii, a …

Cardiometabolic Benefits Of A Non-Industrialized-Type Diet Are Linked To Gut Microbiome Modulation, Fuyong Li, Anissa M. Armet, Katri Korpela, Junhong Liu, Rodrigo Margain Quevedo, Francesco Asnicar, Benjamin Seethaler, Tianna B. S. Rusnak, Janis L. Cole, Zhihong Zhang, Shuang Zhao, Adele Gagnon, Edward C. Deehan, Joao F. Mota, Jeffrey A. Bakal, Russell Greiner, Dan Knights, Nicola Segata, Stephan C. Bischoff, Laurie Mereu, Andrea M. Haqq, Catherine J. Field, Liang Li, Carla M. Prado, Jens Walter

Department of Food Science and Technology: Faculty Publications

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable …

Culturable Microbial Communities In Root Nodules Of Red Alder (Alnus Rubra Bong.) And Scotch Broom (Cytisus Scoparius L.): Patterns Of Diversity And Composition, Felisha (Fay) Rene Pooler

Dissertations and Theses

Endophytes are a hyper diverse group of bacterial or fungal organisms residing within plant tissues without causing visible symptoms of disease. While their overall diversity and ecological functions are not well-understood, some endophytes can provide a range of important benefits to their host such as enhanced growth and increased tolerance to environmental stress. Nitrogen-fixing bacteria residing within nodules--specialized structures on the roots of legumes and actinorhizal plants--play an integral role in the plant microbiome by facilitating nitrogen availability in nutrient-poor environments. Remarkably, the patterns of diversity including both bacterial and fungal endophytes in root nodules are virtually known, except in …

Using Network Pharmacology To Systematically Deduce The Molecular Mechanism Of The Selective Perinucleolar Compartment Inhibitor Ml246, Bhuvnesh P. Sharma, Himanshu N. Singh, Bhupesh Singh, Deepak Parashar, Kuldeep K. Roy, Murali M. Yallapu, Subhash C. Chauhan, Vivek K. Kashyap

Research Symposium

Metarrestin (ML246) is an orally bioavailable synthetic molecule that selectively disrupts the perinucleolar compartment (PNC) structure, and it has showed promise in preclinical studies for metastatic cancer therapy. However, the precise molecular mechanism of ML246 remains poorly understood. We investigated the topological and protein interaction network (PIN) analyses of ML246 to determine the molecular mechanism of ML246. To determine the regulatory effect of ML246 on the rewired PIN of ML246, an intercom was constructed using 25 oncogenic key proteins. These proteins were selected using the reverse pharmacophore matching approach (based on a fit score > 0.502) using the STRING database and …

Trpv1 And Its Co‑Expressed Genes Are Associated With The Progression Of Hepatocellular Carcinoma, Bhuvnesh P. Sharma, Himanshu N. Singh, Sanjay Kumar, Deepak Verma, Deepak Parashar, Murali M. Yallapu, Everardo Cobos, Subhash C. Chauhan, Vivek K. Kashyap

Research Symposium

Background: Hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transient receptor potential vanilloid 1 (TRPV1) is a nonselective Ca²⁺ channel protein widely expressed and plays a significant role in cancer initiation and progression. However, the biological significance of TRPV1 in HCC has not been systematically and comprehensively investigated. This study used deep data mining and transcriptomics analyses to describe the significance of TRPV1 expression and its association with HCC prognosis.

Methods: Download the RNA expression of TRPV1 from the Cancer Genome Atlas (TCGA), Genotype Tissue Expression Atlas (GTEx), Tumor Immune Estimation Resource (TIMER), and the UALCAN …

Impact Of Fresh-Cut Onion Types And Flavonoid Profiles On The Survival Kinetics Of Foodborne Pathogen During Refrigerated Storage, Veerachandra Yemmireddy, Matthew Mancias

School of Earth, Environmental, & Marine Sciences Faculty Publications

This study investigated the effect of onion flavonoid profiles on the growth, survival, and/or death kinetics of foodborne pathogens in fresh-cut onions at 4 °C. Fresh-cut white, yellow, red, and sweet onions were inoculated with separate four-strain cocktail(s) of nalidixic acid-adapted Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes achieving a 4 to 5 log CFU g−1. The samples were stored in clam shell containers at 4 °C and 70 ± 2 % relative humidity for 14 days. Additionally, flavonoid profiles were determined on uninoculated control samples stored under similar conditions using standard chromatography techniques, with quercetin derivatives identified as …

Exploring Oxylipins In Host–Microbe Interactions And Their Impact On Infection And Immunity, Robert J. Neff, Christopher D. Radka

Markey Cancer Center Faculty Publications

Plasma lipids are essential components of biological systems, transported through interactions with proteins to maintain cellular functions. These lipids exist in various forms, such as fatty acids, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenol lipids, derived from dietary intake, adipose tissue, and biosynthesis. While the association between certain fatty acids and cardiovascular diseases has been widely recognized, polyunsaturated fatty acids (PUFAs) exhibit cardioprotective effects, reducing risks of arrhythmias and heart-related mortality. This is due to their role in the production of eicosanoids, which modulate inflammation. Chronic inflammation, particularly in obesity, is significantly influenced by fatty acids, with saturated fatty acids promoting …

Microbial Source Tracking Protocols For Differentiation Of Fecal Bacteria From Cow, Deer, And Horse, Nika Shams, Michael Beach

Symposium of Student Scholars

Microbial source tracking (MST) attempts to identify specific animal sources of fecal contamination in the environment. While traditional fecal coliform enumeration can give a general measure of contamination, the specificity imparted by modern MST provides a more informative assessment of contaminants and their likelihood to affect human health outcomes.

We have been developing an MST system that detects DNA biomarkers from the gram-negative bacterial genus Bacteroides and the family Lachnospiraceae. They are strict anaerobes found in large quantities in the intestines of animals. Unlike E. coli or Enterococci, host-specific strains of Bacteroides and Lachnospiraceae exist. To this end, we …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Thermophilic Microbiota Of Fifth Water Hot Springs: A Genomic Perspective, Ethan Powers, Zack Galbraith, Trever Thurgood

Annual Research Symposium

Geothermal hot springs provide unique microbial habitats characterized by extreme temperatures, variable pH, and diverse geochemical conditions. This study investigates the microbial diversity of three hot spring locations in Diamond Fork Canyon, Utah—Diamond Fork Warm Springs, Fifth Water Hot Springs, and Monk’s Hollow Trailhead—using Oxford Nanopore MinION sequencing of the 16S rRNA gene. Samples were collected in triplicate and analyzed to identify the bacterial composition, with a focus on potential opportunistic pathogens. Our results revealed a diverse microbial community, including members of Pseudomonas, Comamonas, Helicobacter, and Flavobacterium, some of which are known for biofilm formation, antibiotic …

Axl Signaling In Cancer: From Molecular Insights To Targeted Therapies, Monika Yadav, Akansha Sharma, Ketki Patne, Saba Tabasum, Jyoti Suryavanshi, Laxminarayan Rawat, Marc Machaalani, Marc Eid, Rana Singh, Toni Choueiri, Soumitro Pal, Akash Sabarwal

Department of Microbiology and Immunology Faculty Papers

AXL, a member of the TAM receptor family, has emerged as a potential target for advanced-stage human malignancies. It is frequently overexpressed in different cancers and plays a significant role in various tumor-promoting pathways, including cancer cell proliferation, invasion, metastasis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, DNA damage response, acquired therapeutic resistance, immunosuppression, and inflammatory responses. Beyond oncology, AXL also facilitates viral infections, including SARS-CoV-2 and Zika highlighting its importance in both cancer and virology. In preclinical models, small-molecule kinase inhibitors targeting AXL have shown promising anti-tumorigenic potential. This review primarily focuses on the induction, regulation and biological functions of AXL …

Ddo-Adjuvanted Influenza A Virus Nucleoprotein Mrna Vaccine Induces Robust Humoral And Cellular Type 1 Immune Responses And Protects Mice From Challenge, Victoria Gnazzo, Hanaa Saleh, Ítalo A. Castro, Adrianus C. M. Boon, Amelia K. Pinto, James D. Brien, Carolina B. López

Markey Cancer Center Faculty Publications

A challenge in viral vaccine development is to produce vaccines that generate both neutralizing antibodies to prevent infection and cytotoxic CD8+ T-cells that target conserved viral proteins and can eliminate infected cells to control virus spread. mRNA technology offers an opportunity to design vaccines based on conserved CD8-targeting epitopes, but achieving robust antigen-specific CD8+ T-cells remains a challenge. Here, we tested the viral-derived oligonucleotide DDO268 as an adjuvant in the context of a model influenza A virus (IAV) nucleoprotein (NP) mRNA vaccine in C57BL/6 mice. DDO268 when co-packaged with mRNA in lipid nanoparticles is sensed by RIG I-like receptors and …