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Antibiotic resistance in the oral bacterial community
Title
Antibiotic resistance in the oral bacterial community.
Creator
Famuyiwa, Toluleke, Esiobu, Nwadiuto, Jia, Kailiang, Graduate College
Abstract/Description
Purpose: This study was designed to define the antibiotic resistance index of the cultivable oral microbiome to Amoxiacilin Clavulanic acid, Vancomycin, Ciprofloxacin, Clarithomycin, Chlorotetracyclin, Bacitracin, Kanamycin and Tobramycin using a new method adapted from the Kirby Bauer assay. Method: Oral wash samples were collected from 2 current smokers and 2 nonsmokers. Bacterial community were pelleted by centrifugation and used to create a lawn for the assay employing standard disk...
Show morePurpose: This study was designed to define the antibiotic resistance index of the cultivable oral microbiome to Amoxiacilin Clavulanic acid, Vancomycin, Ciprofloxacin, Clarithomycin, Chlorotetracyclin, Bacitracin, Kanamycin and Tobramycin using a new method adapted from the Kirby Bauer assay. Method: Oral wash samples were collected from 2 current smokers and 2 nonsmokers. Bacterial community were pelleted by centrifugation and used to create a lawn for the assay employing standard disk diffusion assay. Zones of inhibition and number of colonies in the zone were recorded. Mean values of inhibition zones were compared to established databases to draw conclusions. Result: The zones of inhibition of Bacitracin antibiotics shows that several bacteria from one of the non smokers were resistant to Bacitracin, while the smokers showed marked susceptibility. Conclusion: The new method developed in our lab yielded consistent set of data which serve as criteria for determining resistance of the oral microbiome to antibiotics. Quite remarkably, it is known that pathogenic beta Streptococci are susceptible to Bacitracin while non-pathogens are not; confirming that healthy persons harbor the healthy strains of streptococci. However the unanswered question is …. Could these normal biota pick up genes and become resistant too? Only time and human habits will decide but we have developed a baseline and an easy method for testing.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00005814
Format
Document (PDF)
Environmental hotspots for antibiotic resistant bacteria arb
Title
Environmental hotspots for antibiotic resistant bacteria arb.
Creator
Dawkins, Karim, Esiobu, Nwadiuto, Graduate College
Abstract/Description
The overuse and misuse of antibiotics in environmental and clinical settings have been a driving force for the prevalence of bacterial resistance. In constant interaction with these chemicals which can harm them, adaptively and inherently, bacteria have devised resistance mechanisms to combat the deleterious effects posed. In the presence of a particular antibiotic, it is expected there will be selection of resistant micro-organisms and their associated resistance genes if present. In this...
Show moreThe overuse and misuse of antibiotics in environmental and clinical settings have been a driving force for the prevalence of bacterial resistance. In constant interaction with these chemicals which can harm them, adaptively and inherently, bacteria have devised resistance mechanisms to combat the deleterious effects posed. In the presence of a particular antibiotic, it is expected there will be selection of resistant micro-organisms and their associated resistance genes if present. In this study, a set of 10 samples were taken from recreational beaches in Ft. Lauderdale, Miami and Hollywood and four different agricultural soils. These soils were enriched after being collected aseptically with three commonly used antibiotics; Ciprofloxacin, Tetracycline and Vancomycin to select for resistant organisms, which produced 29 total samples. A metagenomic analysis was done with 16S rDNA amplification with primers 27F and 1492R which produced 14 out of 29 amplicons producing the expected ~1400 bp fragment from the conserved SSU 16S rDNA region using Agarose gel electrophoresis. From these 14 samples amplified, a second PCR would be run from each enriched antibiotic sample with their respective antibiotic resistance primers eg. vanA-D, tetO and qnrA to identify the resistance genes present expecting that the antibiotic used for enrichment would select for the resistant organisms. Future work includes the sequencing of the amplified resistance genes to help identify novel genetic alterations indicative of new adaptive mechanisms.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00005810
Format
Document (PDF)
In search of environmental hotspots of antibiotic resistance
Title
In search of environmental hotspots of antibiotic resistance.
Creator
Desir, Hedson, Esiobu, Nwadiuto
Date Issued
2013-04-05
PURL
http://purl.flvc.org/fcla/dt/3361076
Subject Headings
Antibiotics resistance in microorganisms, Environmental hotspots
Format
Document (PDF)
DNA Fingerprints and ribotypes of the oral microbiome can distinguish smokers and oral disease patients from healthy non smokers.
Title
DNA Fingerprints and ribotypes of the oral microbiome can distinguish smokers and oral disease patients from healthy non smokers.
Creator
Chakraborty, Shreyasee, Persaud, Verneshia, Vergas, Sonya, Graduate College, Gautier, Gloryanne, Esiobu, Nwadiuto
Abstract/Description
Defining the bacterial communities associated with healthy status will permit rapid detection of shifts associated with disease and foster effective probiotic intervention. This study compares the PCR-RFLP of oral metagenomes and cultured bacterial community, as well as the bacterial diversity profile of smokers, non-smokers and oral disease patients. The goal was to evaluate the stability of bacteria associated with health and capture possible shifts potentially diagnostic of smokers and...
Show moreDefining the bacterial communities associated with healthy status will permit rapid detection of shifts associated with disease and foster effective probiotic intervention. This study compares the PCR-RFLP of oral metagenomes and cultured bacterial community, as well as the bacterial diversity profile of smokers, non-smokers and oral disease patients. The goal was to evaluate the stability of bacteria associated with health and capture possible shifts potentially diagnostic of smokers and oral disease. Oral wash samples were obtained from 5 healthy and 5 smokers twice, 3 months apart. Samples from 5 oral disease patients were also collected. Metagenomic and the genomic DNA of a cultured subset were amplified using primer 1492R and 27F.The generated 16SrRNA gene amplicons were used for arestriction digestion assay and bcloning with the Gene Hunter PCRTrap vector and pCR 4- TOPO cloning kits. The restriction fingerprints were statistically tested using Gel Compare II. The cloned 16S genes were sequenced using the ABI GeneAmp 9700 Thermal cycler. Sequences were analyzed by BLAST on the RDB II database and the HOMD. Sau 3AI and Alu I produced the best distinctive markers of 300 bp in healthy nonsmokers and 500bp in smokers in plate wash communities. The 16S sequence data suggest the presence of a core microbiota in all subjects mostly Streptococcus, Gamella, Candidatuse spp and confirmed that the smokers harbored highly diverse and distinct community Neisseria pharynges, Rothia mucilaginosa. Remarkably, there was a high stability of the fingerprints and diversity profile for smokers and nonsmokers after 3 months.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00005808
Format
Document (PDF)
Impact of Vitamin C on Genistein induced apoptosis in treatment of prostate cancer cells
Title
Impact of Vitamin C on Genistein induced apoptosis in treatment of prostate cancer cells.
Creator
Famuyiwa, Toluleke, Boe, Andrew, Esiobu, Nwadiuto, Graduate College, Kumi-Diaka, James
Abstract/Description
Background: Prostate Cancer, in the absence of skin cancer, is the most prevalent type of cancer found in the male population. Reactive Oxygen Species (ROS) can promote cancer cell proliferation when they are at elevated levels. Vitamin C is a water-soluble antioxidant capable of inhibiting the formation of ROS. Genistein, an isoflavone found in plants, also possesses the ability to inhibit ROS formation. Objective To determine the potential therapeutic synergy between genistein and vitamin C...
Show moreBackground: Prostate Cancer, in the absence of skin cancer, is the most prevalent type of cancer found in the male population. Reactive Oxygen Species (ROS) can promote cancer cell proliferation when they are at elevated levels. Vitamin C is a water-soluble antioxidant capable of inhibiting the formation of ROS. Genistein, an isoflavone found in plants, also possesses the ability to inhibit ROS formation. Objective To determine the potential therapeutic synergy between genistein and vitamin C and investigate mechanism of action of genistein and/or vitamin C. Methods: Trypan blue assay was carried out to know the % of viable cells. Varying concentrations of genistein with a constant concentration of Vitamin C was used to treat LNCaP cells. After treatment of the cells with genistein and Vitamin C, MTT assay of the cancer cells was performed and absorbance read through an ELISA reader. This gives the values needed for interpreting cell viability after treatment. A statistical analysis performed to determine whether the obtained results are statistically significant. Results: The results obtained from our experiments are inconclusive with regards to the impact of Vitamin C on apoptotic cancer cell death following genistein treatment. However the combination of genistein and vitamin C was more efficient in tumor suppression than when the drugs were given separately. Conclusion: This study suggests that treatment of prostate cancer using genistein can be enhanced by adjuvant treatment with vitamin C. This study is of potential clinical success in reducing the cell death by necrosis.
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Date Issued
2015
PURL
http://purl.flvc.org/fau/fd/FA00005876
Format
Document (PDF)
Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms
Title
Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms.
Creator
Dawkins, Karim, Esiobu, Nwadiuto
Date Issued
2016-05-24
PURL
http://purl.flvc.org/fau/fd/FAUIR000138
Format
Citation
A simple method for measuring antibiotic resistance in a community of bacteria
Title
A simple method for measuring antibiotic resistance in a community of bacteria.
Creator
Pelski, Ana, Samaroo, Sheynelle, Varughese, Vipin, Behr, Evalena, Browne, Trisha, Esiobu, Nwadiuto
Abstract/Description
Antibiotic resistant bacteria infiltrate drinking water, increase human exposure, and spread into clinical settings. Regulatory agencies need simple test for ARI to monitor environmental quality. This study is first to measure resistance in a consortium of bacteria, not pure cultures. Our rapid method – “In-the-zone” (ITZ) employs a) the size of zones of inhibition b) identity of bacteria in the zone c) number of resistant clones within zones of inhibition and d) type of antibiotic to compute...
Show moreAntibiotic resistant bacteria infiltrate drinking water, increase human exposure, and spread into clinical settings. Regulatory agencies need simple test for ARI to monitor environmental quality. This study is first to measure resistance in a consortium of bacteria, not pure cultures. Our rapid method – “In-the-zone” (ITZ) employs a) the size of zones of inhibition b) identity of bacteria in the zone c) number of resistant clones within zones of inhibition and d) type of antibiotic to compute ARI. Results can be obtained within 24 - 48 hrs with very little effort. This semester, we repeated the test and validated the weighting of various parameters. The ITZ assay yield consistent and reproducible data on zones of inhibition of bacteria community. The diameter of inhibition zones was the most important parameter distinguishing resistomes of varying ARI. Landfill, manured garden, and waste plant samples scored highest in antibiotic resistance index compared to beach sand.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA0005034
Subject Headings
College students --Research --United States.
Format
Document (PDF)
Microbial Community Resiliency and Role in Sea Level Rise
Title
Microbial Community Resiliency and Role in Sea Level Rise.
Creator
Klein, Christian, Esiobu, Nwadiuto, Office of Undergraduate Research and Inquiry
Abstract/Description
The interphase (littoral zone) of the Florida Everglades and surrounding marine environments are dominated by mangrove forests and mudflats that transition into freshwater communities. As salinity levels change, plant cover of the freshwater community will be adversely affected, but perhaps more importantly, their microbial symbionts responsible for their tolerance to high salinity will be impacted as well. Microbes respond quicker to changing environments and could provide an early warning...
Show moreThe interphase (littoral zone) of the Florida Everglades and surrounding marine environments are dominated by mangrove forests and mudflats that transition into freshwater communities. As salinity levels change, plant cover of the freshwater community will be adversely affected, but perhaps more importantly, their microbial symbionts responsible for their tolerance to high salinity will be impacted as well. Microbes respond quicker to changing environments and could provide an early warning of the loss of resiliency of the Florida coastline ecosystem. For 10 weeks, soil samples from Biscayne National Park will be placed in standardized mesocosms and subject to local conditions like sunlight, tides, plants, increased sea levels, higher salinities, and variant inundation. Standard and variant conditions will be employed on different mesocosms, and weekly DNA extractions of the various soil samples will be analyzed via metagenomic analysis, creating a library of the 16S rRNA community structure over the 10 week period.
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Date Issued
2017
PURL
http://purl.flvc.org/fau/fd/FA00005623
Subject Headings
College students --Research --United States.
Format
Document (PDF)
Elucidation of Microbial Communities From South Florida Beaches Using 16S rRNA Sequence Analysis
Title
Elucidation of Microbial Communities From South Florida Beaches Using 16S rRNA Sequence Analysis.
Creator
Ponukumati, Sushma, Esiobu, Nwadiuto, Florida Atlantic University
Abstract/Description
The composition of marine bacterial communities from South Florida beaches were characterized using 16S rRNA sequence analysis. To compare cultivable and noncultured populations, community genomic DNA was extracted directly from sand and seawater samples and from two cultured equivalents. Only two ofthe 86 (2.3%) direct extracted sequences and 79 of 150 (52.6%) culture sequences belong to known isolates in Ribosomal Database (version 9.0) at 95% confidence level. At low stringency (p=0.70),...
Show moreThe composition of marine bacterial communities from South Florida beaches were characterized using 16S rRNA sequence analysis. To compare cultivable and noncultured populations, community genomic DNA was extracted directly from sand and seawater samples and from two cultured equivalents. Only two ofthe 86 (2.3%) direct extracted sequences and 79 of 150 (52.6%) culture sequences belong to known isolates in Ribosomal Database (version 9.0) at 95% confidence level. At low stringency (p=0.70), the populations cluster into several unknown clads with early divergence, indicating the presence of novel well established bacterial groups. Members of phylum Bacteroidetes, Firmicuites and Proteobacteria were identified, with the latter being the most prevalent in culture. Diversity indices rank Hollywood beach > Fort Lauderdale > Hobie beach. Taxonomic representation indicates marine water as more diverse compared to dry sand and wet sand. A combination of phylogenetic markers will be needed to define the immense diversity of this niche.
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Date Issued
2007
PURL
http://purl.flvc.org/fau/fd/FA00000809
Subject Headings
Marine microbiology--Florida, Evolutionary genetics, Biodiversity--Research, Marine biodiversity conservation
Format
Document (PDF)
Probiotics in aquaculture: An analysis of the bacteria associated with the gut of healthy shrimps, Penaeus spp
Title
Probiotics in aquaculture: An analysis of the bacteria associated with the gut of healthy shrimps, Penaeus spp.
Creator
Yamazaki, Koske, Florida Atlantic University, Esiobu, Nwadiuto
Abstract/Description
A recent surge in the consumption of shrimps has compelled the aquaculture industry to expand greatly. Bacteriosis poses a major challenge to shrimp cultivation. Probiotic control of disease in larvicultures has been on the rise for the past decade; however, there has been little research to provide required frameworks for this promising technology. In this study, the normal gut flora of the commercially important shrimp, Penaeus vannamei, and its relative, P. duorarum was extensively...
Show moreA recent surge in the consumption of shrimps has compelled the aquaculture industry to expand greatly. Bacteriosis poses a major challenge to shrimp cultivation. Probiotic control of disease in larvicultures has been on the rise for the past decade; however, there has been little research to provide required frameworks for this promising technology. In this study, the normal gut flora of the commercially important shrimp, Penaeus vannamei, and its relative, P. duorarum was extensively analyzed to provide a basis for selection of putative probiotic strains. Heterotorphic members of the gut and ambient water were isolated and characterized by culture techniques, microscopy, Biolog biochemical fingerprinting, whole cell crude protein fingerprinting, and 16S rDNA sequence analysis. Non-pathogenic Vibrio harveyi-like strains were prevalent in the gut of both penaied shrimps, regardless of age and source. Community level physiological profiling by principal component analysis showed the gut community was fairly stable throughout shrimp life stages.
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Date Issued
2002
PURL
http://purl.flvc.org/fcla/dt/12927
Subject Headings
Biology, Ecology, Shrimps--Microbiology
Format
Document (PDF)
evaluation of the microbiological quality of sandy beaches: A novel approach
Title
An evaluation of the microbiological quality of sandy beaches: A novel approach.
Creator
Mohammed, Renuka Lisa, Florida Atlantic University, Esiobu, Nwadiuto
Abstract/Description
A novel, 'near-real' time technique; peptide nucleic acid chemilumiscent in situ hybridization (PNA CISH), was developed and validated for detecting, enumerating and identifying potential indicators (Staphyloccus aureus and Pseudomonas aeruginosa) of beach quality. To understand the dynamics of bacterial indicators a plethora of physical, chemical and biological parameters were tested under field and lab conditions. Escherichia coli tagged with green fluorescence protein (GFP) was used to...
Show moreA novel, 'near-real' time technique; peptide nucleic acid chemilumiscent in situ hybridization (PNA CISH), was developed and validated for detecting, enumerating and identifying potential indicators (Staphyloccus aureus and Pseudomonas aeruginosa) of beach quality. To understand the dynamics of bacterial indicators a plethora of physical, chemical and biological parameters were tested under field and lab conditions. Escherichia coli tagged with green fluorescence protein (GFP) was used to assess the impact of wave energy and rainfall on seawater counts. PNA CISH and plate counts correlated strongly (r = 0.94 to r = 0.86). Temperature, salinity, nutrient availability and predation significantly influenced the survival of indicators. Rainfall and wave energy affected the re-suspension of bacteria from sand onto overlying water. Overall PNA CISH provides a reliable rapid method for beach monitoring. The implications of beach topography and sampling time on the numbers of Clostridium perfringens and other potential indicators are discussed. Data suggest a revision of policy for tropical sandy beaches.
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Date Issued
2004
PURL
http://purl.flvc.org/fcla/dt/13117
Subject Headings
Coastal zone management, Coastal ecology, Sand dune ecology, Beaches
Format
Document (PDF)
Survival and decontamination of potential bio-warfare agents on hospital surfaces
Title
Survival and decontamination of potential bio-warfare agents on hospital surfaces.
Creator
Moench, Ian, Florida Atlantic University, Esiobu, Nwadiuto
Abstract/Description
Effective decontamination of infectious agents on critical and other hospital surfaces will drastically reduce nosocomial infections and impacts of any biological attack. This research determined the distribution of multiple species of bacteria on 16 different surfaces in two hospitals over a period of time to identify potential reservoirs of infection. The relative efficacy of current hospital disinfectants on endospores were also evaluated to inform policy. Using simulations of endospore...
Show moreEffective decontamination of infectious agents on critical and other hospital surfaces will drastically reduce nosocomial infections and impacts of any biological attack. This research determined the distribution of multiple species of bacteria on 16 different surfaces in two hospitals over a period of time to identify potential reservoirs of infection. The relative efficacy of current hospital disinfectants on endospores were also evaluated to inform policy. Using simulations of endospore-laden surfaces under laboratory conditions, the effects of exposure time, disinfectant concentration and possible synergies with endospore germination stimulant were evaluated. Keyboards, phones, door handles and bed rails were identified as risky hospital surfaces. The location and use of the surfaces were significant determinants of bacterial load. None of the disinfectants tested was sporicidal (<50% reduction). The results of this unique study provide healthcare personnel with a practical guide to control the spread of infection during peace and bio-warfare times.
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Date Issued
2005
PURL
http://purl.flvc.org/fcla/dt/13215
Subject Headings
Bioterrorism--Health aspects, Emergency management--United States, Health facilities--Sanitation--United States, Bioterrorism--United States--Prevention, Disaster medicine, Disinfection and disinfectants
Format
Document (PDF)
Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures
Title
Co-Cultures of Pseudomonas aeruginosa and Roseobacter denitrificans Reveal Shifts in Gene Expression Levels Compared to Solo Cultures.
Creator
Conway, Crystal A., Esiobu, Nwadiuto, Lopez, Jose V.
Abstract/Description
Consistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-ofprinciple study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies...
Show moreConsistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-ofprinciple study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese)) and two R. denitrificans genes (BetaLact formetallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase) were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations.
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Date Issued
2012
PURL
http://purl.flvc.org/fau/fd/FAUIR000016
Format
Citation
DNA fingerprints of human oral microbiome: a first step towards early diagnosis of oral diseases
Title
DNA fingerprints of human oral microbiome: a first step towards early diagnosis of oral diseases.
Creator
Chakraborty, Shreyasee, Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
This study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non...
Show moreThis study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non-smokers and periodontal disease subjects were evident suggesting the presence of potential indicators of health and poor oral health. Taxon diversity was higher in smokers including members of the genera Rothia, Synechococcus, Neisseria, Thiomargarita and Pyrobaculum but highest in periodontal disease. The two techniques successfully aligned the subjects within appropriate categories (based on their oral microbial genetic patterns)confirming their diagnostic suitability.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00004184, http://purl.flvc.org/fau/fd/FA00004184
Subject Headings
Molecular microbiology., Mouth--Microbiology., Bacterial genetics., Cellular signal transduction., Microbial genomics.
Format
Document (PDF)
ADVANCING THE CULTIVABILITY OF SOIL BACTERIA USING A DYNAMIC SOIL ENVIRONMENT AND SOIL EXTRACT METHOD
Title
ADVANCING THE CULTIVABILITY OF SOIL BACTERIA USING A DYNAMIC SOIL ENVIRONMENT AND SOIL EXTRACT METHOD.
Creator
España, Erick, Brooks, Randy W., Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
Bacteria are inarguably the most ubiquitous and adaptive organisms on the planet. The vast, diverse community of microbes residing in soil are mostly studied using sequencing technologies because over 99% of them are currently uncultivable in the laboratory. This lack of diverse bacterial cultivation presents a serious challenge for modern microbiological and medical science where the discovery of novel antibiotic producers and microbial products has been outpaced by the rise in drug...
Show moreBacteria are inarguably the most ubiquitous and adaptive organisms on the planet. The vast, diverse community of microbes residing in soil are mostly studied using sequencing technologies because over 99% of them are currently uncultivable in the laboratory. This lack of diverse bacterial cultivation presents a serious challenge for modern microbiological and medical science where the discovery of novel antibiotic producers and microbial products has been outpaced by the rise in drug resistance. This study designed and tested two new cost-effective culture systems called the “Dynamic Soil Environment” and Soil Extract Systems with the goal of increasing the cultivable communities of diverse bacteria in a soil sample over standard methods. Illumina MiSeq sequencing and DADA2 pipeline protocols were used to analyze community DNA from cultivated samples and source soil metagenomes. Autoclaved soil extract media in the Soil Extract Experiment yielded a statistically significantly greater Shannon’s (p = 0.008) and Simpson’s diversity (p = 0.007) of bacteria over pH modified (6.4) nutrient agar media over 30 days of incubation. Autoclaved soil extract media was also able to cultivate, on average, 33% of species in bulk soil sequences compared to 27% from standard nutrient agar however these differences weren’t statistically significant. The length of incubation had a lesser effect than media type on yield of bacteria over 30 days in batch culture conditions. Species richness and diversity generally decreased over time except in soil extract samples. In the Dynamic Soil Environment experiment, membrane plates placed on a live soil environment produced a slightly higher diversity than autoclaved membrane plates and control plates without soil, however, these differences were not statistically significant except when analyzed with Chao1 diversity (0.041). Cultivated bacterial diversity and communities differed more according to media type than soil environment with statistically significant differences between standard and pH modified nutrient agar. Media with a 5.8 pH buffer produced a significantly higher relative abundance of the well-known antibiotic-producers, Actinobacteria (t(10) = -5.715, p < .000) and also Proteobacteria (t(10) = -10.127, p < .000). This study establishes cost-effective methods of cultivating more diverse bacterial communities for low-funded laboratories. Culture conditions for the reliable cultivation of higher relative abundances of bacterial groups belonging to Actinobacteria and Proteobacteria are also established with the Dynamic Soil Environment Experiment.
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Date Issued
2019
PURL
http://purl.flvc.org/fau/fd/FA00013304
Subject Headings
Bacteriological Techniques--methods, Bacteriology--Cultures and culture media, Soil
Format
Document (PDF)
Using Synthetic Biology to Create a Safe and Stable Ebola Surrogate for Effective Development of Detection and Therapy Platforms
Title
Using Synthetic Biology to Create a Safe and Stable Ebola Surrogate for Effective Development of Detection and Therapy Platforms.
Creator
Holmes, Douglas, Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
Ebolavirus is responsible for a deadly hemorrhagic fever that has claimed thousands of lives in Africa and could become a global health threat. Because of the danger of infection, novel Ebola research is restricted to BSL-4 laboratories; this slows progress due to both the cost and expertise required to operate these laboratories. The development of a safe surrogate would speed research and reduce risk to researchers. Two highly conserved Ebola gene segments—from the glycoprotein and...
Show moreEbolavirus is responsible for a deadly hemorrhagic fever that has claimed thousands of lives in Africa and could become a global health threat. Because of the danger of infection, novel Ebola research is restricted to BSL-4 laboratories; this slows progress due to both the cost and expertise required to operate these laboratories. The development of a safe surrogate would speed research and reduce risk to researchers. Two highly conserved Ebola gene segments—from the glycoprotein and nucleoprotein genes—were designed with modifications preventing expression while maintaining sequence integrity, spliced into high copy number plasmids, cloned into E.coli, and tested for stability, safety, and potential research applications. The surrogates were stable over 2-3 months, had a negligible mutation rate (<0.165% over the experiment), and were detectable in human blood down to 5.8E3-1.17E4 surrogates/mL. These protocols could be used to safely simulate other pathogens and promote infectious disease treatment and detection research.
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Date Issued
2018
PURL
http://purl.flvc.org/fau/fd/FA00013015
Subject Headings
Ebolavirus, Infectious disease research, Ebola virus disease, Synthetic biology
Format
Document (PDF)
Microbial Aspects of Plant Invasion: An Analysis of Soil Microbial Communities Associated with the Invasive Plant - (Schinus terebinthifolius) Brazilian Pepper Tree Across South-Eastern Florida.
Title
Microbial Aspects of Plant Invasion: An Analysis of Soil Microbial Communities Associated with the Invasive Plant - (Schinus terebinthifolius) Brazilian Pepper Tree Across South-Eastern Florida.
Creator
Dawkins, Karim, Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
The Brazilian pepper tree (BP, Schinus terebinthifolius), introduced to the United States in the 1800s, has since become a category one invasive plant in Florida, aggressively spreading to 3000 km2 of prime habitat. There is a serious dearth of knowledge on whether the rhizobiome plays any roles in the displacement of native flora and the range expansion of BP. This thesis discusses the well-established plant invasion mechanisms of the BP and highlights key emerging mechanisms and gaps in (a)...
Show moreThe Brazilian pepper tree (BP, Schinus terebinthifolius), introduced to the United States in the 1800s, has since become a category one invasive plant in Florida, aggressively spreading to 3000 km2 of prime habitat. There is a serious dearth of knowledge on whether the rhizobiome plays any roles in the displacement of native flora and the range expansion of BP. This thesis discusses the well-established plant invasion mechanisms of the BP and highlights key emerging mechanisms and gaps in (a) the current understanding of the molecular, below-ground processes of BP invasion and (b) studies on the potential role of microbial interactions in the success of BP invasion already established for other select invasive species, and the intervention of soil metagenomic studies to elucidate plant invasive mechanisms. These poorly studied mechanisms could further explain the aggressive spread and resilience of BP and contribute significantly to the development of effective and sustainable control measures, enabling appropriate strategies for restoring native plants.
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Date Issued
2016
PURL
http://purl.flvc.org/fau/fd/FA00004697, http://purl.flvc.org/fau/fd/FA00004697
Subject Headings
Brazilian pepper tree, Ecological risk assessment, Forest ecology, Invasive plants -- Ecology, Nonindigenous pests -- Geographical distribution, Plant invasions
Format
Document (PDF)
UNDERSTANDING THE MICROBIAL ASPECTS OF BRAZILIAN PEPPER TREE (SCHINUS TEREBINTHIFOLIUS) INVASION IN FLORIDA
Title
UNDERSTANDING THE MICROBIAL ASPECTS OF BRAZILIAN PEPPER TREE (SCHINUS TEREBINTHIFOLIUS) INVASION IN FLORIDA.
Creator
Dawkins, Karim, Esiobu, Nwadiuto, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description
Emerging insights on the role of microbiomes in the sustainability of ecosystems and plant cover are transforming knowledge-driven agro-environmental management practices. For more than a century, the Brazilian pepper tree -BP (Schinus terebinthifolius), a category 1 invasive plant in Florida has defied numerous conventional control measures directed at its well-known ecology. This dissertation is one of the pioneer studies designed to determine whether microorganisms play a role in the...
Show moreEmerging insights on the role of microbiomes in the sustainability of ecosystems and plant cover are transforming knowledge-driven agro-environmental management practices. For more than a century, the Brazilian pepper tree -BP (Schinus terebinthifolius), a category 1 invasive plant in Florida has defied numerous conventional control measures directed at its well-known ecology. This dissertation is one of the pioneer studies designed to determine whether microorganisms play a role in the aggressive invasion of BP in Florida and examine potential mechanisms with the goal of creating supplemental restoration tools. To test the hypothesis that enhanced mutualism of Brazilian pepper tree with microbes, compounded by relatively low biotic resistance of Florida soils is a critical driver of its invasion, plant biomass indices, metagenomics analysis of microbial community shifts, electron microscopy of endomycorrhizal infection and qPCR of key rhizobacterial taxa were measured. A multifactorial grow-room experiment was conducted simulating invasion with BP and two Florida natives (Pinus elliottii and Bidens alba) in a sterile, bioinoculant supplemented, and non-sterile control soils with various plant combinations.
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Date Issued
2022
PURL
http://purl.flvc.org/fau/fd/FA00014017
Subject Headings
Brazilian pepper tree, Arbuscular mycorrhizas, Invasive plants
Format
Document (PDF)