Microbiology Commons^™

Correlation Of Gut Alteration With The Progression Of Experimental Autoimmune Encephalomyelitis (Eae) In C57bl/6 Mice, Al Anood Ahmed Al Naqbi

Theses

Background: Experimental autoimmune encephalomyelitis (EAE) is the mouse disease model of multiple sclerosis (MS), a chronic autoimmune disease targeting the central nervous system (CNS) resulting in neuroinflammation, neuroaxonal degeneration, and demyelination. Autoreactive CD4⁺ T cells are known for their role in the pathogenesis of MS. CD8⁺ T cells and NK cells were also found to be associated with the disease.

Aim: There is a limited number of studies investigating the link between gut alterations and immune cells in the gut influencing the outcome of the disease since the vast majority of MS patients experience gastrointestinal (GI) problems. Here, …

Interrogating Antagonistic Differences Among Pseudomonas Aeruginosa Cdia Alleles, Haotian Yang

Master's Theses

Bacteria are complex social organisms that live within mixed communities where microorganisms compete for limited resources. We studied Contact-Dependent Growth Inhibition (CDI), a particular type of competition mediated by a type 5b, or two-partner, secretion system that is widely spread among Gram-negative bacteria. CdiB and CdiA make up the two-partner secretion system that mediates CDI. CdiB translocates CdiA to the cell surface, and CdiA delivers its C-terminal toxin domain to the target cell. The C-terminal toxin (Tox) domain of CdiA is highly diverse. We studied Tox domains of various Pseudomonas aeruginosa clinical isolates. We found different strains that contain unique …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

Synthesis Of 1,2,3-Triazole-Thymol Derivatives As Potential Antimicrobial Agents, Justice Kwaku Addo, Ernest Owusu-Ansah, Nicholas T.K.D. Dayie, Xavier Cheseto, Baldwyn Torto

All Peer-Reviewed Publications

Background: Thymol as a natural biological template can be modified chemically since the hydroxyl group makes it a candidate for structural modification. Thus, this study incorporated the triazole moiety on thymol and the chlorination of thymol moiety to help improve its biological potency. Materials and methods: A series of ten 1,2,3-triazole-thymol derivatives 1–10 were synthesized from thymol, by a click reaction between O-propargyl terminal alkyne of thymol and its chlorothymol with benzyl azide and substituted benzyl azides. Their structures were confirmed by spectroscopic methods (1H-NMR, 13C-NMR, IR, GC-MS-EI/CI and LC-ESI-QTOF-MS). The Well diffusion method using Müeller-Hinton agar plates was used …

Characterisation And Antimicrobial Potential Of Actinobacteria Isolated From Momela Soda Lakes, Tanzania, Witness S. Lema, Ally Mahadhy, Modester Damas, Joan J.E. Munissi, Thomas J. Lyimo

Tanzania Journal of Science

Extreme environments such as soda lakes are potential sources of microbes with biotechnological applications in different sectors. This study aimed at isolation, characterization and investigation of antibacterial potential of actinobacteria from Momela Soda Lakes, at Arusha National Park in Tanzania. One hundred and twenty (120) isolates were recovered from soil and water samples using the dilution plate technique. The isolates were morphologically and biochemically characterized, and further, screened for antimicrobial activity by disc diffusion method as well as the micro dilution technique. Cytotoxic effects were determined using the brine shrimp lethality test. Results showed that, all 120 isolates were Gram-positive …

Chemical Composition And Bioactive Potential Of Extracts From Diospyros Capricornuta F. White Against Aspergillus Flavus And Aspergillus Parasiticus, Princess W. Ngowi, Juma A. Mmongoyo, Lilian D. Kaale

Tanzania Journal of Science

Diospyros capricornuta is an endemic species widely distributed along the coast of Tanzania that is used as food condiments and traditional medicine. The chemical compositions of Diospyros capricornuta leaves, stem-bark, and root-bark extracts; and their bioactive potentials against Aspergillus flavus and Aspergillus parasiticus were investigated. The leaves, stem-bark, and root-bark samples of D. capricornuta were extracted using Soxhlet apparatus and the resultant extracts were analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). A total of 14 compounds were identified from the extracts, whereby 2,4-di-tert-butylphenol was the most abundant compound in all extracts. The growth and aflatoxin production inhibitions against A. flavus and …

Pulse-Field Analysis Diversity Of Extended Spectrum Beta Lactamases Producing Gram Negative Bacteria Isolated From Periplaneta Americana (Cockroaches), Omolara D. Popoola, Moses O. Efuntoye, Georgia C. Agu, Benjamin T. Thomas

Tanzania Journal of Science

Extended spectrum beta lactamase (ESBL) producing bacteria are organisms of public health significance that have been implicated in prolonged hospital stay, treatment failures and higher fatalities. These organisms were originally thought to be widely distributed in hospital, but have since grown in terms of their epidemiological coverage. This study was therefore aimed at using pulse-field gel electrophoresis (PFGE) to understand the diversity of ESBL producing organisms originating from cockroaches in Ago-Iwoye, Nigeria. The diversity was determined by using a set of twenty six (26) ESBL producing bacterial strains isolated from cockroaches sampled in Ago-Iwoye community, Ogun State, Nigeria. PFGE analysis …

Development And Optimization Of An Immunoassay For The Detection Of Antibodies Against Sars-Cov-2 With In-House Recombinant Rbd Protein, Safira Pinaka Pramestika Ratu, Silmi Mariya, Rachmitasari Noviana, Uus Saepuloh, Huda Salahudin Darusman

Makara Journal of Science

COVID-19 caused by SARS-CoV-2 poses a major threat to the global community, particularly in Indonesia. Countermeasures to prevent the spread of this disease have also been implemented, including the implementation of a vaccination program. An immunoassay technique that can be used to analyze antibodies that might develop following vaccination is the indirect enzyme-linked immunosorbent assay (ELISA). We produced the recombinant spike protein used in this study. The optimization comprised adjusted concentrations of spike recombinant protein (5 and 10 ng/mL), blocking agent (2.5% and 5%), and conjugate (1:1000 and 1:5000). The optimal conditions in this study included a spiked concentration of …

Mutation Of Aspergillus Sp. Using Ultraviolet Light And Nitrous Acid For Amylase Production From Banana Peels, Cyprian Erumiseli Oshoma, Johnson Oche Akor, Beckley Ikhajiagbe, Marcel James Ikenebomeh

Makara Journal of Science

Strain improvement through mutagenesis is important in the commercial development of microbial fermentation. This study aimed to produce amylase from banana (Musa sapientum) peels by using mutant Aspergillus sp. strains obtained via ultraviolet (UV) radiation and nitrous acid-based mutagenesis. Results revealed that banana peels pretreated with 0.8 N HCl had a biomass yield of 3.02 g/L and amylase activity of 2.81 U/L. Of the UV mutants, strain AUV1 had the highest biomass and amylase activity of 4.50 ± 0.21 g/L and 3.46 ± 0.14 U/L, respectively. Subsequently, HNO₂ mutants showed that strain ANA6 had 30.64% and …

Forty Years Without Family: Three Novel Bacteriophages With High Similarity To Spp1 Reveal Decades Of Evolutionary Stasis Since The Isolation Of Their Famous Relative, Veronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Gregory P. Krukonis

Biology Faculty Publications

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage–host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more …

Pathogenesis Of Tobacco-Associated Lung Adenocarcinoma Is Closely Coupled With Changes In The Gut And Lung Microbiomes, Casey T Finnicum, Zahraa Rahal, Maya Hassane, Warapen Treekitkarnmongkol, Ansam Sinjab, Rhiannon Morris, Yuejiang Liu, Elizabeth L Tang, Sarah Viet, Jason L Petersen, Philip L Lorenzi, Lin Tan, Joseph Petrosino, Kristi L Hoffman, Junya Fujimoto, Seyed Javad Moghaddam, Humam Kadara

Faculty, Staff and Students Publications

Microbial dysbiosis has emerged as a modulator of oncogenesis and response to therapy, particularly in lung cancer. Here, we investigate the evolution of the gut and lung microbiomes following exposure to a tobacco carcinogen. We performed 16S rRNA-Seq of fecal and lung samples collected prior to and at several timepoints following (nicotine-specific nitrosamine ketone/NNK) exposure in Gprc5a^−/− mice that were previously shown to exhibit accelerated lung adenocarcinoma (LUAD) development following NNK exposure. We found significant progressive changes in human-relevant gut and lung microbiome members (e.g., Odoribacter, Alistipes, Akkermansia, and Ruminococus) that are closely associated with …

Ridinilazole: A Novel, Narrow-Spectrum Antimicrobial Agent Targeting Clostridium (Clostridioides) Difficile, Deirdre A. Collins, Thomas V. Riley

Research outputs 2022 to 2026

Clostridium (Clostridioides) difficile infection (CDI) remains an urgent threat to patients in health systems worldwide. Recurrent CDI occurs in up to 30% of cases due to sustained dysbiosis of the gut microbiota which normally protects against CDI. Associated costs of initial and recurrent episodes of CDI impose heavy financial burdens on health systems. Vancomycin and metronidazole have been the mainstay of therapy for CDI for many years; however, these agents continue to cause significant disruption to the gut microbiota and thus carry a high risk of recurrence for CDI patients. Treatment regimens are now turning towards novel narrow spectrum antimicrobial …

Novel Technologies To Characterize And Engineer The Microbiome In Inflammatory Bowel Disease, Alba Boix-Amorós, Hilarly Monaco, Elisa Sambataro, Jose C. Clemente

Publications and Research

We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, myco - biome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness …

Phylogenetic Diversity Of Animal Oral And Gastrointestinal Viromes Useful In Surveillance Of Zoonoses, Anthony Michael Esposito, Michelle Marie Esposito, Albert Ptashnik

Publications and Research

Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans—from the oral cavity, to the gut, to fecal excretions—have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as …

Frequency Of Bystander Exposure To Antibiotics For Enteropathogenic Bacteria Among Young Children In Low-Resource Settings, Elizabeth T. Rogawski Mcquade, Stephanie A. Brennhofer, Sarah E. Elwood, Timothy L. Mcmurry, Joseph A. Lewnard, Estomih R. Mduma, Sanjaya Shrestha, Najeeha Talat Iqbal, Pascal O. Bessong, Gagandeep Kang

Department of Paediatrics and Child Health

Children in low-resource settings carry enteric pathogens asymptomatically and are frequently treated with antibiotics, resulting in opportunities for pathogens to be exposed to antibiotics when not the target of treatment (i.e., bystander exposure). We quantified the frequency of bystander antibiotic exposures for enteric pathogens and estimated associations with resistance among children in eight low-resource settings. We analyzed 15,697 antibiotic courses from 1,715 children aged 0 to 2 y from the MAL-ED birth cohort. We calculated the incidence of bystander exposures and attributed exposures to respiratory and diarrheal illnesses. We associated bystander exposure with phenotypic susceptibility of E. coli isolates in …

The Cryptococcus Neoformans Flc1 Homologue Controls Calcium Homeostasis And Confers Fungal Pathogenicity In The Infected Hosts, Piotr R. Stempinski, Kristie D. Goughenour, Lukas M. Du Plooy, J. Andrew Alspaugh, Michal A. Olszewski, Lukasz Kozubowski

Open Access Publishing Fund

Cryptococcus neoformans, an opportunistic yeast pathogen, relies on a complex network of stress response pathways that allow for proliferation in the host. In Saccharomyces cerevisiae, stress responses are regulated by integral membrane proteins containing a transient receptor potential (TRP) domain, including the flavin carrier protein 1 (Flc1), which regulates calcium homeostasis and flavin transport. Here, we report that deletion of C. neoformans FLC1 results in cytosolic calcium elevation and increased nuclear content of calcineurin-dependent transcription factor Crz1, which is associated with an aberrant cell wall chitin overaccumulation observed in the flc1Δ mutant. Absence of Flc1 or inhibition …

Genetic Determinants Of Carotenoid Pigmentation In The Opportunistic Pathogen Mycobacterium Kansasii, Niklas Janisch

Dissertations, Theses, and Capstone Projects

Mycobacterium kansasii (Mk) is an opportunistic pulmonary pathogen causing infections, predominantly in immunocompromised people, with symptoms similar to those caused by its close relative Mycobacterium tuberculosis (Mt). In contrast to the latter, little work has been done on Mk genetics and even less on its defining characteristic of photochromogenicity, the controlled expression of carotenoid pigments in response to light exposure.

This work represents major progress in the investigation of pigmentation-related genetic factors in Mk. We report the creation of a large-scale, random transposon-insertion mutant library of Mk and its subsequent screening for mutants with an aberration in the …

Elucidation Of Gene Essentiality And Genetic Determinants Of Intrinsic P-Aminosalicylic Acid Resistance In Mycobacterium Kansasii, Keith J. Levendosky

Dissertations, Theses, and Capstone Projects

Mycobacterium kansasii (Mk) is an opportunistic pathogen capable of causing tuberculosis-like pulmonary disease in immunocompromised individuals and those with other risk factors including chronic obstructive pulmonary disease or malignancy. Mk is frequently isolated from man-made water sources where it forms resilient biofilms, posing a health risk to these susceptible individuals. Despite its medical relevance as an environmental pathogen, and a close phylogenetic relationship with the obligate pathogen Mycobacterium tuberculosis (Mtb), few studies to date have probed the molecular biology and genetics of Mk. Here, we sought to apply a transposon (Tn) mutagenesis tool to dissect …

Whole-Genome Sequencing Links Clostridium (Clostridioides) Difficile In A Single Hospital To Diverse Environmental Sources In The Community, Su-Chen Lim, Deirdre Collins, Korakrit Imwattana, Daniel R. Knight, Sicilia Perumalsamy, Natasza M.R. Hain-Saunders, Papanin Putsathit, David Speers, Thomas Riley

Research outputs 2022 to 2026

To investigate if Clostridium (Clostridioides) difficile infection (CDI), traditionally thought of as hospital-acquired, can be genomically linked to hospital or community environmental sources, and to define possible importation routes from the community to the hospital.

In 2019, C. difficile was isolated from 89/300 (29.7%) floor and 96/300 (32.0%) shoe sole samples at a tertiary hospital in Western Australia. Non-toxigenic C. difficile ribotype (RT) 010 predominated among floor (96.6%) and shoe sole (73.2%) isolates, while toxigenic RT 014/020 was most prevalent among contemporaneous clinical cases (33.0%) at the hospital. Whole-genome sequencing and high-resolution core genome single nucleotide polymorphism (cgSNP) …

Esculin Hydrolysis Negative And Tcda-Only Producing Strains Of Clostridium (Clostridioides) Difficile From The Environment In Western Australia, Nirajmohan Shivaperumal, Daniel R. Knight, Korakrit Imwattana, Grace O. Androga, Barbara J. Chang, Thomas V. Riley

Research outputs 2022 to 2026

Background and Aims: Clostridium (Clostridiodes) difficile clade 3 ribotype (RT) 023 strains that fail to produce black colonies on bioMérieux ChromID agar have been reported, as well as variant strains of C. difficile that produce only toxin A. We have recently isolated strains of C. difficile from the environment in Western Australia (WA) with similar characteristics. The objective of this study was to characterize these strains. It was hypothesized that a putative β-glucosidase gene was lacking in these strains of C. difficile, including RT 023, leading to white colonies. Methods and Results: A total of 17 environmental isolates of C. …