Microbiology Commons^™

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Effect Of Red And Blue Light On Lipid, Protein, Carbohydrate, And Pigment Contents Of Navicula Sp., Sofyan Maulana, Aulia Setyo Nurul Hida, Ismia Wulandari, Siti Mudrikah, Dedy Kurnianto, Khusnul Qonita Maghfiroh, Ria Amelia, Tia Erfianti, Renata Adaranyssa Egistha Putri, Irika Devi Anggraini, Septhian Marno, Eko Agus Agus Suyono

Makara Journal of Science

Light quality critically modulates the physiology of diatoms, influencing photosynthetic efficiency and metabolite synthesis. This study examines how monochromatic red (620–750 nm) or blue (450–495 nm) light affects the biochemical profiles and pigment production in Navicula sp. versus white light (control). Cultures were grown in sterile f/2 medium, and biomass was tracked via OD₆₈₀. Biochemical analyses included lipids (Bligh and Dyer method), carbohydrates (phenol-sulfuric acid assay), proteins (Bradford assay), and pigments (spectrophotometric quantification). The growth dynamics were modeled using logistic and Gompertz equations. No significant differences in OD-based growth rates, carbohydrates, proteins, or lipids content were observed with …

Characteristics And Potential Indigenous Bacteria Isolated From Shallot Farming In Brebes Regency As Diazinon Pesticide Remediation Agents, Wahyu Purbalisa, Dian Hendrayanti, Wahida Annisa Yusuf

Makara Journal of Science

Diazinon is an organophosphate pesticide that is widely used by shallot farmers in Brebes Regency. Due to its toxicity, diazinon residue in agricultural lands as well as plants’ cultivation is harmful to humans and the environment. Using indigenous soil bacteria as a remediation agent is an alternative solution to overcome diazinon contamination. Firstly, this study aimed to characterize isolates from diazinon-contaminated shallot farming. The second objective was to test the diazinon tolerance of the isolates in various diazinon concentrations. Isolation was carried out using nutrient agar (NA) media containing diazinon concentrations of 5, 25, 50, and 100 ppm. The characterization …

Artificial Intelligence In Head And Neck Cancer: Towards Precision Medicine, Jacob Hagen, Logan Hornung, William Barham, Supratik Mukhopadhyay, Adam Bess, Kevin Contrera, Devraj Basu, Vlad Sandulache, Guillaume Spielmann, Sagar Kansara

Faculty, Staff and Students Publications

Over the past 20 years, the capabilities of artificial intelligence (AI) have gained significant interest. While AI has been implemented to various degrees in several disciplines, its unique applications in head and neck cancer (HNC) remain underdeveloped. This narrative review examines the existing body of literature regarding the use of AI in HNC. Studies to date have demonstrated AI’s utility across multiple phases of the HNC treatment continuum. Despite its promise, integrating AI into clinical practice faces several challenges, including concerns about system integrity, generalizability, privacy, and bias. In this review, we address these challenges and offer insights into future …

Clinical Applications Of Probiotics: A Comprehensive Review Of Benefits And Challenges, Riyam Wissam Hassan

Maaen Journal for Medical Sciences

Probiotics are beneficial microorganisms that help balance microbes in intestines and promote growth beneficial bacteria, they vary between bacteria, yeasts, and fungi and they are helpful to human health when taken in adequate and suitable amounts. In addition to maintaining intestinal health and help with digestion and absorption, also inhibiting development and preventing spread of harmful microorganisms. It exists in different forms, in the intestines and in the foods, products fermented, and in the pharmaceutical supplements. Because human health depends largely on the interaction between humans and these microorganisms known as probiotics, it has found that these organisms have vital …

Metagenomic Characterization Of Gut Microbiota In Children With Autism Spectrum Disorder: Microbial Signatures And Modulation By Anti-Inflammatory Diet And Probiotics, Marysol Valencia-Buitrago, Rodrigo Dias Oliveira-Carvalho, Valbert Cardoso, Jessica Triviño-Valencia, Luisa Matilde Salamanca-Duque, Vanessa Martínez-Díaz, Jovanny Zabaleta, Narmer Fernando Galeano-Vanegas, Carlos Andrés Naranjo-Galvis

School of Medicine Faculty Publications

Background: Autism Spectrum Disorder (ASD) is increasingly associated with alterations in gut microbiota, intestinal permeability, and immune dysregulation. However, integrative studies exploring these mechanisms in Latin American populations are lacking. Objective: To characterize gut microbiota profiles in Colombian children with ASD and evaluate the effects of two microbiota-targeted interventions, an anti-inflammatory diet and a probiotic formulation, on microbial diversity and taxonomic composition. Methods: In a two-phase study, shotgun metagenomic sequencing was performed on fecal samples from 23 children with ASD and 7 typically developing (TD) controls. In the second phase, 17 children with ASD were randomized to receive a 12-week …

Structural Basis For Promoter Recognition By Pseudomonas Phage Dev Virion Associated Rna Polymerase, Brittney Bird

All ETDs from UAB

Bacteriophage DEV, a member of the Schitoviridae family, encodes a large virion-associated RNA polymerase (vRNAP) and shows significant potential for use in phage therapy. However, many aspects of DEV’s biology remain poorly understood, especially how it regulates transcription once inside the host. Recent work in our lab suggests that gene product 71 (gp71) functions as a DNA-dependent vRNAP. Analogous to the vRNAP of coliphage N4, gp71 likely initiates transcription by recognizing single-stranded DNA templates that contain early gene hairpin promoters. Based on this, my working hypothesis is that specific interactions between gp71 and the DEV early promoters PE1 and PE5 …

Characterizing The Role Of Pneumococcal Surface Protein A And Humoral Immunity To Biofilm Antigens During Streptococcus Pneumoniae Colonization, Jessica Lane

All ETDs from UAB

Streptococcus pneumoniae (Spn), or “the pneumococcus”, is a Gram-positive bacterium that colonizes the upper respiratory tract as a pathobiont. Spn is a deadly human pathogen, and one of the leading etiological agents of community-acquired pneumonia (CAP). One virulence factor of Spn is pneumococcal surface protein A (PspA), a choline-binding protein (CBP) at the surface of the bacteria that interacts with the host environment. Here, we demonstrated a novel role for PspA involving adhesion to dying host nasal epithelial cells via a multimeric complex with host lactoferrin (LF) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found that the PspA-GAPDH complex aggregated the bacteria …

The Role Of The Glycerol Metabolism Regulator Glpr On Pseudomonas Aeruginosa’S Physiology, Nicholas Jordan Evans

All ETDs from UAB

Chronic infections with Pseudomonas aeruginosa are a leading cause of morbidity and mortality in people with cystic fibrosis. P. aeruginosa persists in the CF lung through adaptations, including altering the expression of metabolic genes to acquire nutrients that are abundant in the CF airway. Glycerol in the airway is imported and metabolized by proteins encoded in the glp regulon, which is regulated in part by GlpR. The loss of GlpR was previously shown to increase biofilm development in a P. aeruginosa CF isolate compared to a wound isolate. In the first half of this work, we investigated the influence that …

Influenza A Virus Increases Susceptibility To Streptococcus Pneumoniae By Damaging The Airway Epithelium, Erin Yepsen Earnhardt

All ETDs from UAB

Influenza A Virus (IAV) is commonly complicated by secondary bacterial infections with Streptococcus pneumoniae (Spn), leading to increased morbidity and mortality. Recent work from our lab demonstrates that an IAV-induced loss of cystic fibrosis transmembrane conductance regulator (CFTR) in the airway disrupts the rheostatic properties of the airway surface liquid (ASL). In cystic fibrosis, caused by mutations in the CFTR gene, there is an increase in the bacterial burden of the airway. However, the underlying mechanisms and damage caused by IAV-induced CFTR dysfunction in the airway remains unknown. Using a primary differentiated human bronchial airway epithelial cell culture (HBEC) system, …

Lineage-Associated Zinc Metalloprotease B And Its Impact On Cardiac Damage Elicited During Invasive Pneumococcal Disease, Jennifer Nichelle Luck

All ETDs from UAB

During invasive disease, certain strains of Streptococcus pneumoniae (Spn) can invade the myocardium, damaging cardiomyocytes and predisposing patients to life-threatening cardiac complications. To identify genetic loci involved in pneumococcal cardio-virulence, we performed a bacterial genome-wide association study using 825 genomes corresponding to 17 distinct Spn lineages associated with varying rates of cardiac complications during hospitalization for pneumonia. This led to the identification of an allele of zmpB, the gene encoding Zinc metalloprotease B (ZmpB). Infection of mice with a ZmpB deficient mutant, i.e., TIGR4ΔzmpB, found that ZmpB was required to form foci of infection in the heart, i.e., cardiac microlesions. …

Barriers And Timely Postoperative Radiation Therapy In Head And Neck Cancer, Megan T Nguyen, Emily Kistner-Griffin, Reid Demass, Bhisham S Chera, Chanita Hughes Halbert, Katherine R Sterba, Elizabeth G Hill, Brian Nussenbaum, Anthony J Alberg, Vlad C Sandulache, David J Hernandez, Ryan S Jackson, Sidharth V Puram, Russel Kahmke, Nosayaba Osazuwa-Peters, Gail Jackson, Sue S Yom, Evan M Graboyes

Faculty, Staff and Students Publications

Importance: Initiation of postoperative radiation therapy (PORT) within 6 weeks of surgery is associated with improved outcomes among patients with head and neck squamous cell carcinoma. However, the relationship of barriers to care with timely PORT is unknown.

Objective: To categorize barriers to timely PORT, evaluate the association of barriers to care with initiation of timely PORT, and describe the primary reason for delay among patients without timely PORT.

Design, setting, and participants: This prospective cohort study at a US academic medical center included adults with head and neck squamous cell carcinoma undergoing curative-intent surgery with an indication for PORT. …

Probiotic Biogeography In The Neonatal Intestine, Sierra Hansen

All ETDs from UAB

Neonatal infection remains a leading cause of both neonatal morbidity and mortality worldwide, particularly in preterm infants. Probiotic bacteria have been demonstrated to protect against the development of neonatal intestinal dysbiosis, however, formulations and efficacy vary substantially, highlighting a critical gap in the current understanding of the mechanisms governing probiotic efficacy in this population. This gap is exacerbated by regulatory standards which favor economic expansion over scientific rigor. Furthermore, current studies on probiotic efficacy largely rely on indirect or relative readouts of intestinal bacterial burden. Herein, we directly quantify the probiotic effects of Ligilactobacillus murinus V10 and Escherichia coli Nissle …

Detection Of Heterogeneous Resistance Mechanisms To Tyrosine Kinase Inhibitors From Cell-Free Dna, Heather A Parsons, Conor Messer, Katheryn Santos, Jakob Weiss, David Merrell, Brian P Danysh, Melissa E Hughes, Gregory J Kirkner, Ashka Patel, Julian Hess, Kerry Sendrick, Chip Stewart, Elizabeth Grant, Kristy Schlueter-Kuck, Albert Grinshpun, Nikhil Wagle, Jamunarani Veeraraghavan, Jose Pablo Leone, Rachel A Freedman, Otto Metzger, Rachel Schiff, Eric P Winer, Sara M Tolaney, Mothaffar Rimawi, Ian E Krop, Gad Getz, Nancy U Lin

Faculty, Staff and Students Publications

Though there has been substantial progress in the development of anti-human epidermal growth factor receptor 2 (HER2) therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experience disease progression and cancer-related death. HER2-directed tyrosine kinase inhibitors can be highly effective therapies for patients with HER2-positive MBC; however, an understanding of resistance mechanisms is needed to better inform treatment approaches. We performed whole-exome sequencing on 111 patients with 73 tumor biopsies and 120 cell-free DNA samples to assess mechanisms of resistance. In 11 of 26 patients with acquired resistance, we identified alterations in previously …

Analyzing The Role Of A Dual-Function Diguanylate Cyclase / Phosphodiesterase For Attachment And Motility In Agrobacterium Tumefaciens, Priya Aryal

Theses and Dissertations

Cyclic diguanylate monophosphate (c-di-GMP) is a second messenger that is responsible for attachment and motility in many prokaryotic systems and controls the signaling pathway for the motile to sessile transition in many bacteria. Many c-di-GMP-metabolizing proteins are diguanylate cyclases (DGCs), responsible for the synthesis of c-di-GMP and characterized by a c-di-GMP synthesizing domain, e.g., GGDEF domain. Other c-di-GMP-metabolizing proteins contain c-di-GMP degradative domains, e.g., EAL, characterized by phosphodiesterase activity (PDE). In Agrobacterium tumefaciens, out of 31 predicted proteins regulating the c-di-GMP level, this project focuses on the predicted dual-function DGC/PDE, DcpB. We hypothesized that DcpB plays a role in the …

Results Of Tor001: An Open-Label Single Patient Study Using Targeted Bacteriophage Therapy For The Treatment Of A Chronic Urinary Tract Infection, Jonathan D Cook, Payton B Hooey, Keiko C Salazar, Justin R Clark, Umesh Jain, Carlos Fernando, Hanjeong Harvey, Alexander Cervantes, Stephanie Omagari, Udi Blankstein, Andrew M Kropinski, Alan R Davidson, Karen L Maxwell, Lori L Burrows, Austen L Terwilliger, Anthony W Maresso, Greg J German

Faculty, Staff and Students Publications

Chronic urinary tract infections are persistent bacterial infections with the potential to drive antibiotic resistance. Like other persistent bacterial infections, intracellular bacterial reservoirs and biofilm formation hinder the clearance of pathogens despite long courses of antibiotic therapy. New strategies for treatment of these persistent infections are needed. Here we describe the results of an open-label individual patient study using bacteriophage therapy to treat a chronic urinary tract infection in an immunocompetent 72-year-old woman without underlying urolithiasis or indwelling devices. We co-administered HP3.1, HP3, and ES19 bacteriophages with demonstrated in vitro activity via bladder instillation, orally, and as a topical formulation. …

Enhancing The Care Of Patients With Bone And Joint Infections Through Educational Interventions, Neel B. Shah, Jessica Seidelman, Katherine Belden, Elizabeth Thottacherry, Allison Lastinger, Priya Nori, Ronald M. Beaulieu, Don Bambino Geno Tai

Division of Infectious Diseases and Environmental Medicine Faculty Papers

Musculoskeletal infections represent a significant proportion of the clinical workload for infectious diseases (ID) providers, often presenting complex diagnostic and therapeutic challenges. Many providers may feel inadequately prepared to manage these conditions, which require a nuanced understanding of microbiology, musculoskeletal anatomy, surgical intervention, and orthopedic hardware. We implemented a pair of educational interventions including an online library of high-yield musculoskeletal ID literature and an educational podcast. © The Author(s) 2025. Published by Oxford University Press on behalf of Infectious Diseases Society of America.

The Role Of Liver Macrophages In Viral Liver Pathogenesis, Alexis Brantly, Kyle Yeakle, Michael J. Bouchard, Peter J. Gaskill, Michael R. Nonnemacher

Kimmel Cancer Center Faculty Papers

Liver macrophages play important roles in the pathophysiology of liver fibrosis and hepatocellular carcinoma. However, liver macrophages are a heterogenous population and have differing roles in maintenance of liver function and response in disease. In a healthy liver, macrophages play a critical role in antigen processing, maintaining tolerance to the high levels of gut-derived bacterial products, and regulating inflammation through cytokine response. However, macrophages also play a critical role in liver pathology, specifically in the context of viral infection. The liver is targeted by multiple viruses, including human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, which dysregulate macrophage …

Evaluation Of Tracheal And Cecal Microbial Composition In Heat Stressed Broilers Supplemented With Phytogenic Additives, Andressa Silveira Stein

Graduate Theses and Dissertations

The rise in global temperatures has become a concern due to its significant impact on the agricultural sector, including poultry production. Heat stress caused by high temperatures directly affects animal welfare, health and productivity, leading to major losses in the poultry sector. In broilers, heat stress affects feed consumption, weight gain, mortality and may also lead to changes in the microbiome, which can increase the predisposition to disease and impact the overall performance of these animals. The aim of this thesis was to reproduce field conditions, simulating an increase in temperature, and to evaluate possible changes in the respiratory and …

Elephant Endotheliotropic Herpesvirus 2 Infection In 5 African Elephants (Loxodonta Africana) At Multiple North American Zoological Institutions, Taylor J Willis, Anne Burgdorf-Moisuk, Maren Connolly, Jan Raines, Cameron Ratliff, Zoltan S Gyimesi, Erica Lipanovich, Genevive A Dumonceaux, Kathryn L Perrin, Lauren L Howard, Matthew E Kinney, Kirk Suedmeyer, Erin Latimer, Tiffany L Kim, Jessica R Watts, Jie Tan, Paul Ling

Faculty, Staff and Students Publications

Objective: To acknowledge that elephant endotheliotropic herpesvirus (EEHV) is a well-recognized major threat to Asian elephants (Elephas maximus) and can cause acute and often fatal hemorrhagic disease (HD). Historically, EEHV-HD has been less frequently identified in African elephants (Loxodonta africana). This case series describes 5 recent cases of EEHV2 infection in African elephants within managed care at 5 North American institutions.

Animals: 5 African elephants (L africana).

Clinical presentation: The cases involved 4-, 7-, and 10-year-old males that died despite receiving aggressive medical therapy and 4- and 14-year-old females that survived. Clinical signs included lethargy, decreased appetite, lameness, changes in …