Microbiology Commons^™

Special Issue: Biofilm Composition And Applications, Bindu Subhadra

Faculty Publications - Biological Sciences

Generally, EPS may be hydrophobic, although it can be both hydrophilic and hydrophobic [9]. Since EPS is highly hydrated, it helps to prevent desiccation in some natural biofilms [9]. Currently, there is increasing interest in the use of biofilm-forming microorganisms as bioremediation agents, as they convert hazardous environmental substances (pollutants such as oil spills; organic pollutants such as polycyclic aromatic hydrocarbons and polychlorinated biphenyls; and polychlorinated ethenes, heavy metals, dyes, explosives, pesticides, and pharmaceutical products) into less toxic or harmless compounds [20,29]. [...]excess nutrients (nitrogen and phosphorus) in the wastewater also need to be removed to avoid anoxia [32]. [...]the …

The Role Of L-Alanine Signaling In Aspergillus Fumigatus Biofilm Adherence, Carbon Catabolism, And Echinocandin Susceptibility., Joshua D. Kerkaert

Dartmouth College Ph.D Dissertations

Aspergillus fumigatus is a saprophytic filamentous fungus that participates in environmental carbon and nitrogen cycles through the degradation of complex organic substrates. In addition to its ecological role, A. fumigatus is the primary causative agent of a spectrum of diseases depending on the immune status of the individual, the most lethal of which is invasive aspergillosis (IA). Treatment strategies for IA are limited and far too frequently fail. Despite the high rates of treatment failure, antifungal resistance remains relatively low, albeit rising at a concerning rate. Insights into this discrepancy between the rate of treatment failure and the rate of …

Molecular Mechanisms Underlying Mucosal Attachment And Colonization By Clostridioides Difficile, Ben Sidner

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium which causes gastrointestinal disease and is a leading cause of nosocomial infections. Although infection typically occurs following antibiotic therapy, in recent years there has been an increase in infections which are not preceded by antibiotic use. Additionally, community-associated infections and rates of disease recurrence have increased. While it is understood that a healthy gastrointestinal microbiota provides protection against infection, the molecular mechanisms which underly C. difficile's ability to colonize and persist in the gut are mostly unknown. Building on work from others that suggests C. difficile associates with the outer mucus …

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 …

Methanogen Metabolic Flexibility, Sean R. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …

Jatropha Tanjorensis A Flora Of Southeast Nigeria: Isolation And Characterization Of Naringenin And Validation Of Bio-Enhanced Synergistical Activity Of Α- Tocopherol Toward Clinical Isolates Of Resistant Bacterial, Ikechukwu Kingsley Ijoma, Vincent Ishmael Egbulefu Ajiwe

Makara Journal of Science

Jatropha tanjorensis is among the rich floras of Southeast Nigeria and used by ethnic people to treat infections and manage health conditions. Ethnomedicine has long been employed in the treatment of ailments caused by bacterial pathogens. Studies showed that the incorporation of synthetic α-tocopherol to an antibacterial agent improves its activity. However, knowledge about the antibacterial-enhanced activity of plant-based α-tocopherols, especially those isolated from Jatropha tanjorensis, is limited because of the different bioactivities of synthetic and natural α-tocopherols. To determine the phytochemicals in J. tanjorensis, we carried out the structural elucidation of its leaf extracts. Naringenin and α-tocopherol …

A Mathematical Model And Sensitivity Analysis Of Lassa Fever With Relapse And Reinfection Rate, Latifat M Erinle-Ibrahim, Olukayode Adebimpe, Waheed O Lawal, Joshua O Agbomola

Tanzania Journal of Science

In this research paper, we depict an unprecedented four-dimensional ordinary differential equation modeling the dynamic transmission of the Lassa fever virus incorporating relapse and reinfection rate. Recent studies showed that the recovered individuals from Lassa fever can again be susceptible; which contradicted the common assumptions made by different researchers on modeling of Lassa fever. So, this article corrects and states the implications of the assumptions on the population density. The numerical simulations unveil the effect of relapse, reinfection, and treatment rate in the affected population. Performing sensitivity analysis suggests all new incorporated parameters can impact the infection dynamics substantially. The …

Molecular Identification Of Cryptococcus Neoformans Isolates From House Environments Of Hiv-Infected Patients In An Urban Area, Indonesia: A First Report, Machrumnizar Machrumnizar, Robiatul Adawiyah, Tjahjani Natriana, Darma Imran, Mohammad Muslim, Sjamsuridzal Wellyzar, Retno Wahyuningsih

Makara Journal of Science

Cryptococcus neoformans isolates were previously obtained from pigeon droppings in Jakarta. This study aimed to determine another source of infection and describe the supporting niche of the fungus. The occurrence of C. neoformans was evaluated in 110 samples of decaying wood and leaves, tree hollow debris, dust, and bird droppings. Yeasts isolates were collected from 22 houses of HIV-infected patients. The isolates were identified based on culture characteristics, an assimilation test, and URA5 restriction fragment length polymorphism polymerase chain reaction. The spatial analysis was conducted in geographical information system to determine dominant house and environmental factors. Seven of the 120 …

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

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 …

Presence Of Blaper-1 And Blaveb-1 Beta-Lactamase Genes Among Isolates Of Pseudomonas Aeruginosa From Burn And Trauma Hospital Peshawar, Pakistan, Suleman Khan, Samiyah Tasleem, Alfarah Rehmat Ullah,, Sarwat Moon, Saad Alghamdi, Raina Saad Suliman, Muhammad Ateeq, Muhmmad Salman, Anas S. Dablool,, Banan Atwah, Farkad Bantun

Journal of Bioresource Management

Pseudomonas aeruginosa spp are the most prevalent bacteria that cause nosocomial infections in hospitals. Most antibiotics, including novel new β-lactams, are already resistant to them, and they can become resistant during treatment, which can make the treatment fail. P. aeruginosa isolates from ICU patients who had Per-1 and VEB-1 were the main focus of this study. These two ESBLs are the two most common in ICU patients who had them. 50 isolates were gathered from Peshawar's LRH ICU facilities in the year 2021. The antibiotic susceptibility test was conducted in accordance with the Clinical and Laboratory Standards Institute's standards (CLSI). …

Assessing The Human-Health Risk Of Exposure To Pathogens From Beach Sands, Javier Federico Gallard-Góngora

USF Tampa Graduate Theses and Dissertations

Fecal contamination at recreational beaches impacts the health of beachgoers, through the introduction of disease-causing microorganisms, and the well-being of communities dependent on income from recreational beach activities. Beach ecosystems are also impacted by sewage through the introduction of nutrients that can cause abnormal increases in autochthonous microorganisms which can impact the population of larger organisms in the ecosystem. Fecal contamination is introduced into sand via untreated sewage, direct deposition of human feces into sand, runoff, and deposition of animal feces into sand. The introduction of fecal contamination into sand exposes individuals to pathogens (disease causing microorganisms) which can result …

Seroprevalence Of Sars-Cov-2 Antibodies, The Gut Microbiome, And Peripherally Circulating Cytokines In Pregnant Hispanic Females, Tina Susanna Mutka

USF Tampa Graduate Theses and Dissertations

Pregnant Hispanic females have been disproportionately impacted by SARS-CoV-2 andhave experienced high rates of asymptomatic or mildly symptomatic, unrecognized infection. Acute SARS-CoV-2 infection has been associated with gut microbiome changes and altered peripherally circulating cytokine levels in symptomatic, non-pregnant individuals.

This study investigated the seroprevalence of anti-SARS-CoV-2 IgG antibodies in a sample of pregnant Hispanic females (n = 197). A sub-sample of SARS-CoV-2 seropositive and seronegative pregnant Hispanic females were followed across pregnancy and their bacterial gut microbiome was characterized, and cytokine levels measured to investigate relationships between SARS-CoV-2 serostatus, the gut microbiome, and peripherally circulating cytokine levels across pregnancy. …

Nitrogen Fixation Rates In Forested Mountain Streams: Are Sediment Microbes More Important Than Previously Thought?, Erica A. H. Bakker, Carmella Vizza, Clay Arango, Sarah S. Roley

Biology Faculty Scholarship

1. Biological nitrogen (N) fixation, the microbial conversion of N₂ gas to ammonia, makes N available to food webs. Low-N streams often have a high relative abundance of N-fixing taxa, suggesting that N fixation is an important N source in these systems. Despite this potential, stream N fixation has not been well-characterised, particularly compared to lakes and marine environments. One unknown is the relative contributions of various N-fixing organisms, particularly heterotrophic microbes.
2. In low-N streams in the Cascade Mountains (Washington, USA), three groups of N-fixers predominate: cyanobacteria (Nostoc paramelioides) colonies that house a midge symbiont (Cricotopus spp.), …

Antibiotic-Resistant Escherichia Coli And EnterococcusSpp. In Sand And Water At Tampa Bay Beaches, Jennifer K. Sabater

USF Tampa Graduate Theses and Dissertations

As antibiotic resistance in the environment continues to rise there is an increased concern that infections may become harder to treat as bacteria acquire genes for multidrug resistance. Recreational beach waters in the Tampa Bay area are routinely monitored by the Florida Department of Environmental Protection for the presence of fecal indicator bacteria (FIB) such as Escherichia coli and enterococci. Exceedances of beach action values (BAV) 235 CFU/100 mL (E. coli) and 70 CFU/100 mL (enterococci) indicate the presence of fecal contamination which is associated with an increased risk of disease for beachgoers. Antibiotic-resistant E. coli and Enterococcus spp. have …

The Role Of The Gut-Brain Axis In Alzheimer's Disease: A Narrative Review, Leila Karout

University Honors Theses

The importance of the gut microbiome in health has become increasingly recognized as more research points to the strong association between an imbalanced gut microbial composition and a diseased state. Alzheimer's Disease burdens millions, and the rate of growth is expected to increase. However, current treatment methods are less than ideal and do not offer a substantial benefit to patients' quality of life. Additionally, there are gaps in the current understanding of Alzheimer's Disease pathogenesis. Research on the relationship between gut microbiota and neurodegeneration provides a different perspective on the pathogenesis and treatment methods for dementia, such as Alzheimer's Disease. …

Exploring Melatonin As A Treatment For Oral Ulcers, William H. Sutherland

Undergraduate Honors Theses

The hormone melatonin is best known for its role in the sleep-wake cycle, but its anti-inflammatory and antioxidant effects have significant implications that have not been fully explored in oral health. Some studies use melatonin to treat gastrointestinal ulcers, including duodenal ulcers and oral mucositis, but we found no study reporting its effects on more common oral ulcers, like aphthous stomatitis. We hypothesize that the anti-inflammatory and antioxidant characteristics of melatonin could effectively prevent and heal oral ulcers. In this paper, we review the literature on melatonin to propose its use as a treatment for oral ulcers. We also include …

Investigating The Antagonistic Activity Of Asymptomatic Bacteriuria Against Uropathogenic E. Coli., Ciara Kenneally

ORBioM (Open Research BioSciences Meeting)

Asymptomatic bacteriuria (ABU) is the presence of bacteria in urine, resembling a state of commensalism. Bacteria are characterised as ABU when they have been isolated from two consecutive urine samples (≥ 10⁵ CFU/ml) from individuals, but without symptoms attributable to a urinary tract infection (UTI). ABU Escherichia coli strains have evolved from uropathogenic ancestors and lack virulence factors associated with uropathogenic E. coli (UPEC). UPEC are the main etiological agent of urinary tract infections (UTIs), attributable to > 80% of cases. The frequency at which multidrug-resistant UPEC are isolated is affecting guidelines for use of former first-line antibiotics for UTIs, …

Biowill - Characterising Willow Bark Bio-Actives For Skin Therapies, Arnold Marisa

ORBioM (Open Research BioSciences Meeting)

Willow bark is considered as a disposable by-product when processing willow for biomass. Willow (Salix) is known to contain high value bioactive compounds which include salicin and its derivatives, and other phytochemicals of interest such as polyphenols and flavonoids. The plant is historically known as the primary source of salicylates to which the well-known drug aspirin is derived from. The work forms part of the Interreg project BioWILL, which is focused on integrated “Zero Waste” biorefinery utilising all fractions of willow feedstock for the production of biochemicals and renewable energy. This project aims to investigate the crude and …

Investigation Of The Antimicrobial Activity Of Coagulase Negative Staphylococci Of Human Origin, Ellen Twomey

ORBioM (Open Research BioSciences Meeting)

Coagulase Negative Staphylococci (CoNS) are significant members of the human microbiome and have been identified as a source of bacteriocins, small bioactive substances recognised for their antimicrobial properties. In this study we screened a bank of 37 human derived CoNS for the production of these peptides with emphasis on identifying those with the ability to inhibit the growth of Methicillin Resistant Staphylococcus aureus (MRSA). Deferred antagonism assays confirmed potential antimicrobial activity in all 37 isolates against sensitive indicator M. luteus, with nine inhibiting the growth of at least one MRSA strain they were overlaid against. Tests performed with the …

Short Chain Fatty Acid Combination Treatment Protects Against 6-Ohda Induced Decrease In Neurite Growth In An In Vitro Model Of Parkinson’S Disease., Alex Morris

ORBioM (Open Research BioSciences Meeting)

Title: Short chain fatty acid combination treatment protects against 6-OHDA induced decrease in neurite growth in an in vitro model of Parkinson’s disease.

Authors: Alex Morris¹, Louise M. Collins^1,2,3, Gerard W. O’Keeffe², Caitriona M. Guinane¹

¹ Department of Biological Sciences, Munster Technological University (MTU), Cork, Ireland.

² Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland.

³ Department of Physiology, University College Cork, Cork, Ireland.

Background: Parkinson’s disease (PD) is a neurodegenerative disorder characterized by dopaminergic neuron degeneration. This leads to motor dysfunction which is accompanied by gastrointestinal comorbidities such as constipation …

Effect Of Sub-Inhibitory Concentrations Of Nitrofurantoin, Ciprofloxacin And Trimethoprim On In-Vitro Biofilm Formation In Uropathogenic Escherichia Coli, Shane Whelan

ORBioM (Open Research BioSciences Meeting)

The purpose of the current study was to determine the effect of sublethal concentrations of nitrofurantoin, ciprofloxacin and trimethoprim on biofilm formation in 57 uropathogenic Escherichia coli strains (UPEC).

The MIC of nitrofurantoin, ciprofloxacin and trimethoprim was determined for 57 UPEC isolates. Biofilm formation for each isolate with and without sub-lethal concentrations of each antibiotic was then quantified, and the statistical significance of changes in biofilm formation was ascertained by way of a Dunnett's test.

The effects of sub-MIC antibiotics on biofilm formation of UPEC were variable. A total of 22.8% of strains were induced to form biofilm by nitrofurantoin, …

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 …

Investigation Of The Urobiome For The Production Of Novel Antimicrobials Against Uropathogenic E. Coli (Upec), Jennifer Jones

ORBioM (Open Research BioSciences Meeting)

BACKGROUND: Urinary tract infections (UTIs) are one of the most common bacterial infections globally with antibiotic treatment becoming increasingly less effective. The urobiome remains a relatively understudied niche as a source of potentially novel antimicrobials (e.g., bacteriocins). Improvements to bacterial culturing and sequencing techniques have highlighted the potentially rich source of alternative treatments and control strategies to target uropathogenic E. coli (UPEC).

MATERIALS AND METHODS: (a) BAGEL 4 was used for bioinformatic screening of the genomes of urobiome isolates to identify bacteriocin gene clusters (BGC).

(b) Expanded quantitative urine culture (EQUC) was used to culture mid-stream urine samples to isolate …

'Investigating The Effect Of Cell-Free Supernatant Of Probiotic Strains On The Viability Of Pancreatic Cancer Cell Lines', Claire M. Doocey

ORBioM (Open Research BioSciences Meeting)

Background

Pancreatic cancer (PC) is a prevalent cancer accounting for over 450,000 deaths globally in 2020, and is associated with limited treatment options and high mortality rates. Mounting evidence implicates the human microbiome in tumorigenesis and cancer progression with key players including Helicobacter pylori in gastric cancer and Fusobacterium nucleatum in colorectal cancer and PC. Current research, however, also suggests a potential role for certain microbial residents in oncological treatment and biotherapeutic development. Recent studies have shown a link between cell-free supernatants (CFS) from probiotic strains and cancer cell death, suggesting their potential in targeting the tumour microenvironment. Probiotic genera …

Tunable Diode Laser Absorption Spectroscopy As An Alternative Method For Non-Invasive Sterility Detection In Ready To Feed Infant Milk Products, Peter Myintzaw

ORBioM (Open Research BioSciences Meeting)

Background: The potential application of rapid, non-destructive, and user-friendly TDLAS technology to detect contamination in commercially sterile dairy beverages where visual inspection is not possible was investigated for the first time. The TDLAS equipment uses laser light to monitor carbon dioxide changes due to microbial growth in the container headspace which has the advantage of being rapid and non-destructive. This study aimed to provide detailed scientific evidence for the application of TDLAS technology as a method to determine product sterility in real food products.

Methods: TDLAS growth detection of Bacillus fengqiuensis, Candida albicans, Lactococcus lactis, Microbacterium …

Application Of Fructans-Degrading Lachancea Fermentati Fst5.1 As An Alternative To Baker’S Yeast In The Production Of A Low-Fodmap Whole Wheat Bread., Małgorzata Borowska

ORBioM (Open Research BioSciences Meeting)

FODMAPs are a group of poorly absorbed dietary carbohydrates comprised of easily fermentable oligo-, di-, monosaccharides and polyols. When consumed, they can exert gastrointestinal symptoms of pain, flatulence, or an irregular bowel movement in individuals with irritable bowel syndrome. Whole wheat bread is an excellent source of proteins, vitamins, polyphenols, and other nutrients, but its consumption is restricted in a low-FODMAP diet due to high fructans content. Although alternatives exist, these are primarily gluten-free, often inferior in terms of quality, nutritional profile, and consumer acceptance. Bioprocessing using microbial fermentation has a proven capacity to reduce FODMAPs in cereal products, but …

Complex Role Of Microbiome In Pancreatic Tumorigenesis: Potential Therapeutic Implications, Suneetha Amara, Li V. Yang, Venkataswarup Tiriveedhi, Mahvish Muzaffar

Biology Faculty Research

Pancreatic cancer (PC) is the fourth leading cause of cancer-related mortality with limited diagnostic and therapeutic options. Although immunotherapy has shown promise in the treatment of several cancers, its role in pancreatic cancer is rather limited. Several studies have focused on determining the role of the tumor microenvironment with cancer-cell-intrinsic events and tumor-infiltrating immune cellular properties. However, in the past decade, there has been emerging research aimed at delineating the role of the host microbiome, including the metabolites from microbes and host responses, on pancreatic tumorigenesis. Importantly, there is emerging evidence suggesting the beneficial role of a gut microbiome transplant …

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 …

Analysis Of Soxs In S. Typhimurium By Transposon Mutagenesis, Joel Hanns, Brenda Pratte, Lon Chubiz Phd, Lauren Daugherty

Undergraduate Research Symposium

The mar-sox-rob regulon has been implicated in transcriptional regulation of several stress responses, such efflux of antibiotics, enzymes that break down reactive oxygen species, repression of biofilm formation, or repression of motility through downregulation of flagellar expression. This system is conserved among enteric bacteria and has been studied in species, such as E. coli and S. typhimurium. Some of these mechanisms can be costly and slow cell growth while increasing the probability of survival through tolerance of toxic environments. SoxS works in coordination with SoxR to respond to redox stress encountered by the cell. Interestingly, the overexpression of SoxS …