Life Sciences Commons^™

A Microbiome Analysis Of The Relationship Among Crayfish Ectosymbionts And Their Environment, John Hoverson

Senior Honors Theses

The purpose of this project was to determine if there are differences present between the α-diversities of the crayfish microbiome and its surrounding water and sediment. Furthermore, this project sought to discover if these differences hold when microbiomes are evaluated between crayfish of first and second stream orders. Finally, this project sought to determine if the presence of branchiobdellidan ectosymbionts on the crayfish caused further differences in the crayfish microbiome. While the hypothesized patterns between crayfish, ectosymbionts, and stream order were not found to exist, a significantly different microbiome was observed between water, sediment, and crayfish, and the α-diversity of …

Exploration Of The Role Of Microbiome Structure, Metabolism, And Modification In Black Band Disease Etiology, Patricia Waikel

FIU Electronic Theses and Dissertations

The coral microbiome plays an integral role in coral health. Modification of the microbiome is thought to alter susceptibility to disease. Black Band Disease (BBD), is polymicrobial, mat forming, and affects reef building coral globally. Dominated by the cyanobacterium Roseofilum reptotaenium, it has been noted to increase in virulence with increasing temperatures, making BBD of particular concern in the face of climate change-induced warming seas. The active sulfur cycle of BBD makes dimethylsulfoniopropionate (DMSP), a widely available source of sulfur in the marine environment, of particular interest in the study of BBD. Traditional infection studies require field collection and …

Tick-Borne Pathogens Shape The Native Microbiome Within Tick Vectors, Abdulsalam Adegoke, Deepak Kumar, Cailyn Bobo, Muhammad Imran Rashid, Aneela Zameer Durrani, Muhammad Sohail Sajid, Shahid Karim

Faculty Publications

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Ticks are blood-feeding arthropods and transmit a variety of medically important viral, bacterial, protozoan pathogens to animals and humans. Ticks also harbor a diverse community of microbes linked to their biological processes, such as hematophagy, and hence affect vector competence. The interactions between bacterial and/or protozoan pathogens and the tick microbiome is a black-box, and therefore we tested the hypothesis that the presence of a protozoan or bacterial pathogen will alter the microbial composition within a tick. Hence, this study was designed to define the microbial composition of two tick species, …

Shifts In The Microbiota Associated With Male Mosquitoes (Aedes Aegypti) Exposed To An Obligate Gut Fungal Symbiont (Zancudomyces Culisetae), Jonas Frankel-Bricker

University Author Recognition Bibliography: 2020

Research characterizing arthropod-associated microbiota has revealed that microbial dynamics can have an important impact on host phenotypic traits. The influence of fungi on these interactions are emerging as targets for research, especially in organisms associated with global human health. A recent study demonstrated colonization of a widespread gut fungus (Zancudomyces culisetae) in a larval mosquito (Aedes aegypti) digestive tract affected microbiomes in larvae and newly emerged adult females (Frankel-Bricker et al. Appl Environ Microbiol, 2020. https://doi.org/10.1128/AEM.02334-19) but did not investigate these processes in males. The objective of the study presented here was to assess fungal influences …

Causality In Microbiomes, Md Musfiqur Rahman Sazal

FIU Electronic Theses and Dissertations

No abstract provided.

Laboratory Colonization By Dirofilaria Immitis Alters The Microbiome Of Female Aedes Aegypti Mosquitoes, Abdulsalam Adegoke, Erik Neff, Amie Geary, Montana Ciara Husser, Kevin Wilson, Shawn Michael Norris, Guha Dharmarajan, Shahid Karim

Faculty Publications

Background

The ability of blood-feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered with, or enhanced by, the arthropod’s native microbiome. Mosquitoes transmit viruses, protozoan and filarial nematodes, the majority of which contribute to the 17% of infectious disease cases worldwide. Dirofilaria immitis, a mosquito-transmitted filarial nematodes of dogs and cats, is vectored by several mosquito species including Aedes aegypti.

Methods

In this study, we investigated the impact of D. immitis colonization on the microbiome of laboratory reared female Ae. aegypti. Metagenomic analysis of the V3–V4 variable …

Microbiomes Of Caribbean Octocorals Vary Over Time But Are Resistant To Environmental Change, Mark Mccauley, Colin R. Jackson, Tamar Goulet

Faculty and Student Publications

The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorgonians exposed to environmental perturbations. We found that seven shallow water Caribbean gorgonian species maintained distinct microbiomes and predominantly harbored two bacterial genera, Mycoplasma and Endozoicomonas. Representatives of these taxa accounted for over 70% of the sequences recovered, made up the three most common operational taxonomic units (OTUs), and were present in …

Evaluation Of Maternal Diet And Its Effect On Milk Composition And Piglet Health And Growth Performance, Shana Barnett

Department of Animal Science: Dissertations, Theses, and Student Research

Both graduate research and graduate teaching duties work together to help to develop a graduate student’s skills both in the classroom and on their research experiments. Being both a GTA and GRA allows a student to form more sound hypotheses, connect better with students, and better understand their own research.

During the time as a GTA and GRA four surveys were developed to analyze different groups of students and their learning environment and two animal experiments were conducted to evaluate maternal diet and its effect on milk composition and piglet health and growth performance

The surveys given to students consisted …

Identification And Analysis Of Feather Degrading Bacteria: A Search For Keratinase Genes, Nehal Navali

Honors Scholar Theses

Over two million tons of feather waste is generated annually by the poultry industry, the majority of which goes into landfills due to the difficulty of degrading its major component keratin. Although a portion of feather waste is eliminated via incineration or chemical treatment, the use of Feather Degrading Bacteria (FDB) has been proposed as a cheap and eco-friendly alternative. FDBs have been consistently isolated from the feather microbiome of birds and contain genes coding for the specialized protein keratinase which is able to degrade feathers. By doing so, feather waste, which is rich in nutrients, can be repurposed as …

Using Bioinformatics Tools To Evaluate Potential Risks Of Food Allergy And To Predict Microbiome Functionality, Mohamed Abdelmoteleb

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

Novel foods and Genetically Engineered (GE) organisms are being developed for nutritional, industrial, and environmental applications. Dietary interventions have been used recently to mitigate methane emissions in ruminants. In this project, bioinformatics tools have been used to answer two main questions. The first question is the potential allergy risks for consumption of novel foods and GE organisms. The second question is the effects of dietary interventions on microbiome functionality related to methane production in ruminants.

To answer the first question, regulatory authorities in the United States and Europe now expect an evaluation of new proteins in novel foods or genetically …

The Relationship Between The Cervical Microbiome And Cervical Cancer Risk In Sub-Saharan Africa, Cameron Klein

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

Despite ongoing efforts, sub-Saharan Africa faces a higher cervical cancer burden than anywhere else in the world. Besides HPV infection, definitive factors of cervical cancer are still unclear. Dysbiosis of the cervicovaginal microbiota, particularly involving sexually transmitted infections, is associated with increased cervical cancer risk. Notably, HIV infection, which is prevalent in sub-Saharan Africa, greatly increases risk of cervicovaginal dysbiosis and cervical cancer. To better understand and address cervical cancer in sub-Saharan Africa, a better understanding of the regional cervicovaginal microbiome is required. In this study, I establish the relationship between cervical cancer, HPV, HIV, cervicovaginal infections, and the cervicovaginal …

How Can We Change Gut Microbiota For Healthy Lives?, Elizaveta Shmakova

Scientific Communication News

No abstract provided.

Go With Your Gut: The Role Of Gut Microbiota In Health, Lydia Bangerter, Mateja R. Savoie-Roskos, Jeffrey Chapman, Abbigail Sundell, Carrie Durward

All Current Publications

Living within your gastrointestinal tract (gut) are about 100 trillion bacterial cells—your gastrointestinal microbiota—a host of bacteria that play a vital role in your body (Ghaisas, Maher, & Kanthasamy, 2016). Your gut microbiome is responsible for a wide variety of functions that contribute to overall health and may be linked to many chronic diseases including cancer, obesity, and cardiovascular disease (Ghaisaset al., 2016; Peregrin, 2013). This fact sheet will discuss the role the gut microbiome plays in various aspects of health and how to improve your gut health.

Investigating Microbiomes And Developing Direct-Fed Microbials To Improve Cattle Health, Alison Bartenslager

Department of Animal Science: Dissertations, Theses, and Student Research

Over the last decade, global beef production has increased to meet the protein needs of the growing population. As a result, the intensification of beef cattle production systems has resulted in broad spectrum prophylactic use of antibiotics and growth promoting agents. With increased concern around antimicrobial resistance (AMR) and emergence of novel pathogenic strains of bacteria, it is critical to understand disease progression and associated changes in the microbiome to develop novel therapeutic alternatives to reduce antibiotic use and control disease. One such approach that is currently being investigated is the development of novel direct-fed microbial strains to outcompete pathogens …

Variation In The Microbiota Associated With Daphnia Magna Across Genotypes, Populations, And Temperature, Jonas Frankel-Bricker, Michael J. Song, Maia J. Benner, Sarah Schaack

University Author Recognition Bibliography: 2020

Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism’s biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any …

Preliminary Microbiome Analysis Of Freshwater Bivalves From Turnbull National Wildlife Refuge, Dechen Edwards

2020 Symposium Posters

Eukaryotic hosts and their associated microbes exhibit variable relationships. Some are driven by well-documented benefits including microbial contributions to host digestion; others are less understood. In this project, we seek to understand how a host’s microbiome is differentiated from the surrounding, free-living microbial community and whether this process is altered by the presence of pollution. Here we present a protocol developed for the extraction, isolation, and identification of the microbial population found in freshwater “fingernail” clams (Sphaeriidae) based on modified methods from the Earth Microbiome Project and studies of freshwater amphibian and marine bivalve microbiomes. We first developed …

Scalable Profiling And Visualization For Characterizing Microbiomes, Camilo Valdes

FIU Electronic Theses and Dissertations

Metagenomics is the study of the combined genetic material found in microbiome samples, and it serves as an instrument for studying microbial communities, their biodiversities, and the relationships to their host environments. Creating, interpreting, and understanding microbial community profiles produced from microbiome samples is a challenging task as it requires large computational resources along with innovative techniques to process and analyze datasets that can contain terabytes of information.

The community profiles are critical because they provide information about what microorganisms are present in the sample, and in what proportions. This is particularly important as many human diseases and environmental disasters …

Comparative Analysis Of Rhizosphere Microbiomes Of Southern Highbush Blueberry (Vaccinium Corymbosum L.), Darrowâs Blueberry (V. Darrowii Camp), And Rabbiteye Blueberry (V. Virgatum Aiton), Jiangang Li, Olga V. Mavrodi, Jinfeng Hou, Chazden Blackmon, Ebrahiem M. Babiker, Dmitri V. Mavrodi

Faculty Publications

Plants are inhabited by millions of parasitic, commensal, and mutualistic microorganisms that coexist in complex ecological communities, and profoundly affect the plant’s productivity, health, and capacity to cope with environmental stress. Therefore, a better understanding of the rhizosphere microbiome may open a yet untapped avenue for the rational exploitation of beneficial plant–microbe interactions in modern agriculture. Blueberries encompass several wild and cultivated species of shrubs of the genus Vaccinium that are native to North America. They are grown commercially for the production of fruits, which are considered a health food due to the rich content of minerals, trace elements, and …

A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides (Clostridium) Difficile Infection In Mice, Whereas A High-Carbohydrate Diet Protects, Chrisabelle C. Mefferd, Shrikant S. Bhute, Jacqueline R. Phan, Jacob V. Villarama, Dung M. Do, Stephanie Alarcia, Ernesto Abel-Santos, Brian P. Hedlund

Chemistry and Biochemistry Faculty Research

Clostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and …

Host Population Genetics And Biogeography Structure The Microbiome Of The Sponge Cliona Delitrix, Cole Easson, Andia Chaves-Fonnegra, Robert W. Thacker, Jose Lopez

Biology Faculty Articles

Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted by the excavating sponge Cliona delitrix. A total of 53 samples, previously used to demarcate the population genetic structure of C. delitrix, were selected from two locations in the Caribbean Sea and …

A High-Throughput Lc-Ms/Ms Method For The Measurement Of The Bile Acid/Salt Content In Microbiome-Derived Sample Sets, Thomas D. Horvath, Sigmund J. Haidacher, Kathleen M. Hoch, Jennifer M. Auchtung, Anthony M. Haag

Department of Food Science and Technology: Faculty Publications

Due to the physicochemical properties of bile acids/salts (i.e., hydrophobic and ionizable), the application of reverse-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods are ideally suited for the measurement of these compounds in a host of microbiologically-relevant matrices. Here, we provide a detailed bioanalytical protocol that contains several modifications of a method previously described by Wegner et al. [1]. Briefly, this modified method exhibits the following advantages for the measurement of cholic acid (CA), taurocholic acid (TCA), and deoxycholic acid (DCA) in microbiome-relevant sample matrices: i) fecal sample processing has been streamlined by the elimination of lyophilization and manual homogenization steps; …

Metabolic Feedback Inhibition Influences Metabolite Secretion By The Human Gut Symbiont Bacteroides Thetaiotaomicron, Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron (B. theta) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic …

Wild Primate Microbiomes Prevent Weight Gain In Germ-Free Mice, Dimitrios N. Sidiropoulos, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Tonya L. Ward, Abigail J. Johnson, Pajau Vangay, Dan Knights, Purna C. Kashyap, Yibo Xian, Amanda E. Ramer-Tait, Jonathan B. Clayton

Department of Food Science and Technology: Faculty Publications

Background: The gut microbiome harbors trillions of bacteria that play a major role in dietary nutrient extraction and host metabolism. Metabolic diseases such as obesity and diabetes are associated with shifts in microbiome composition and have been on the rise in Westernized or highly industrialized countries. At the same time, Westernized diets low in dietary fiber have been shown to cause loss of gut microbial diversity. However, the link between microbiome composition, loss of dietary fiber, and obesity has not been well defined.

Results: To study the interactions between gut microbiota, dietary fiber, and weight gain, we transplanted captive and …

Single-Arm, Non-Randomized, Time Series, Single-Subject Study Of Fecal Microbiota Transplantation In Multiple Sclerosis, Phillip A. Engen, Antonia Zaferiou, Heather Rasmussen, Ankur Ankub, Stefan J. Green, Louis F. Fogg, Christopher B. Forsyth, Shohreh Raeisi, Bruce Hamaker, Ali Keshavarzian

Department of Nutrition and Health Sciences: Faculty Publications

Emerging evidence suggests intestinal microbiota as a central contributing factor to the pathogenesis of Relapsing-Remitting-Multiple-Sclerosis (RRMS). This novel RRMS study evaluated the impact of fecal-microbiota-transplantation (FMT) on a broad array of physiological/clinical outcomes using deep metagenome sequencing of fecal microbiome. FMT interventions were associated with increased abundances of putative beneficial stool bacteria and short-chain-fatty-acid metabolites, which were associated with increased/improved serum brain-derived-neurotrophic-factor levels and gait/walking metrics. This proof-of-concept single-subject longitudinal study provides evidence of potential importance of intestinal microbiota in the pathogenesis of MS, and scientific rationale to help design future randomized controlled trials assessing FMT in RRMS patients.

Rhizosphere Microbiome Of Arid Land Medicinal Plants And Extra Cellular Enzymes Contribute To Their Abundance, Abdul Latif Khan, Sajjad Asaf, Raeid M. M. Abed, Yen Ning Chai, Ahmed N. Al-Rawahi, Tupan Kumar Mohanta, Ahmed Al-Rawahi, Daniel P. Schachtman, Ahmed Al-Harrasi

Department of Agronomy and Horticulture: Faculty Publications

Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low …

Identification Of Simplified Microbial Communities That Inhibit Clostridioides Difficile Infection Through Dilution/Extinction, Jennifer M. Auchtung, Eva C. Preisner, James Collins, Armando I. Lerma, Robert A. Britton

Department of Food Science and Technology: Faculty Publications

The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile. To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to resist C. difficile colonization after challenge, as measured by 􏰀100-fold reduction in levels of C. difficile in challenged communities. We screened 76 simplified communities diluted from cultures of six fecal donors and identified 24 simplified communities that inhibited C. difficile colonization in vitro. Sequencing revealed that simplified communities were composed of …

How The Cervical Microbiota Contributes To Cervical Cancer Risk In Sub-Saharan Africa, Cameron Klein, Crispin Kahesa, Julius Mwalselage, John T. West, Charles Wood, Peter C. Angeletti

Nebraska Center for Virology: Faculty Publications

Despite ongoing efforts, sub-Saharan Africa faces a higher cervical cancer burden than anywhere else in the world. Besides HPV infection, definitive factors of cervical cancer are still unclear. Particular states of the cervicovaginal microbiota and viral infections are associated with increased cervical cancer risk. Notably, HIV infection, which is prevalent in sub-Saharan Africa, greatly increases risk of cervicovaginal dysbiosis and cervical cancer. To better understand and address cervical cancer in sub-Saharan Africa, a better knowledge of the regional cervicovaginal microbiome is required This review establishes current knowledge of HPV, HIV, cervicovaginal infections, and the cervicovaginal microbiota in sub-Saharan Africa. Because …

Hiding In Plain Sight: The Globally Distributed Bacterial Candidate Phylum Pauc34f, Michael L. Chen, Eric D. Becraft, Maria Pachiadaki, Julia M. Brown, Jessica K. Jarett, Josep M. Gasol, Nikolai V. Ravin, Duane P. Moser, Takuro Nunoura, Gerhard J. Herndl, Tanja Woyke, Ramunas Stepanauskas

Research outputs 2014 to 2021

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while …

Coproid Predicts The Source Of Coprolites And Paleofeces Using Microbiome Composition And Host Dna Content, Maxime Borry, Bryan Cordova, Angela Perri, Marsha Wibowo, Tanvi Prasad Honap, Jada Ko, Kate Britton, Linus Girdland-Flink, Robert C. Power, Ingelise Stuijts, Domingo C. Salazar-García, Courtney Hofman, Richard Hagan, Thérèse Samdapawindé Kagoné, Nicolas Meda, Helene Carabin, David Jacobson, Karl Reinhard, Cecil Lewis, Aleksandar Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hübner, Christina Warinner

Karl Reinhard Publications

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal …

The Utilization Of Eukaryotic Cell Types In Microbiomes For Semen, Vaginal Fluid, And Menstrual Blood Identification Using 18s Rdna, Ines Benaissa

Master of Science in Forensic Science Directed Research Projects

The accurate identification of body fluids is vital for crime scene investigation and forensic analysis. While many body fluids can be presumptively identified, there is a lack of confirmatory testing for verification. Therefore, the purpose of this study was to determine if body fluids (menstrual blood, vaginal fluid, and semen) could be differentiated based on their eukaryotic microbial communities. The target area of interest was the V9 hyper-variable region of 18S ribosomal DNA (18S rDNA). The samples were extracted, barcoded using a duel-index strategy, and PCR amplified before undergoing high throughput sequencing using the Illumina Miseq FGx instrument. The samples …