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This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities

This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities in the deep-sea water of the Pacific Ocean. Both RT-PCR and qRT-PCR approaches were employed to detect expression of the genes involved in photosynthesis of photoautotrophic organisms. Positive results were obtained and further proved the functional activity of these detected photosynthetic microbes in the deep-sea. Metagenomic and metatranscriptomic data was obtained, integrated, and analyzed from deep-sea microbial communities, including both prokaryotes and eukaryotes, from four different deep-sea sites ranging from the mesopelagic to the pelagic ocean. The RNA/DNA ratio was employed as an index to show the strength of metabolic activity of deep-sea microbes. These taxonomic and functional analyses of deep-sea microbial communities revealed a `defensive' life style of microbial communities living in the deep-sea water. Pseudoalteromonas sp.WG07 was subjected to transcriptomic analysis by application of RNA-Seq technology through the transcriptomic annotation using the genomes of closely related surface-water strain Pseudoalteromonas haloplanktis TAC125 and sediment strain Pseudoalteromonas sp. SM9913. The transcriptome survey and related functional analysis of WG07 revealed unique features different from TAC125 and SM9913 and provided clues as to how it adapted to its environmental niche. Also, a comparative transcriptomic analysis of WG07 revealed transcriptome changes between its exponential and stationary growing phases.
ContributorsWu, Jieying (Author) / Meldrum, Deirdre R. (Thesis advisor) / Zhang, Weiwen (Committee member) / Abbaszadegan, Morteza (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2013
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Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore,

Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.
ContributorsHalcomb, Michael Jordan (Author) / Chen, Qiang (Thesis director) / Steele, Kelly (Committee member) / Barrett, The Honors College (Contributor) / College of Letters and Sciences (Contributor)
Created2015-05
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Lophomonas is a genus of flagellated parabasalids that exist as commensal symbionts in the hindguts of a variety of pest cockroaches. The genus contains two species: Lophomonas blattarum and Lophomonas striata. The two species differ by way of bacterial ectosymbionts that attach to the outside of L. striata, giving rise

Lophomonas is a genus of flagellated parabasalids that exist as commensal symbionts in the hindguts of a variety of pest cockroaches. The genus contains two species: Lophomonas blattarum and Lophomonas striata. The two species differ by way of bacterial ectosymbionts that attach to the outside of L. striata, giving rise to a striated and spindle-shaped appearance. As the attachment of bacterial symbionts prohibits L. striata from taking up large food particles in the same manner as L. blattarum, it is likely the two species differ in which metabolic genes they possess. Here, a comparison of transcriptomes between the two Lophomonas species show slight differences between the species. Metagenomic analysis of L. striata also presents the possibility of L. striata ectosymbionts as belonging to the genus Parabacteroides.
ContributorsNguyen, Leann (Author) / Gile, Gillian (Thesis advisor) / Dada, Nsa (Committee member) / Wideman, Jeremy (Committee member) / Arizona State University (Publisher)
Created2023
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Bats are a highly diverse mammal species with a dense virome and fascinating immune system. The following project utilizes metagenomics in order to identify DNA viruses present in populations of silver-haired bats and Mexican free-tailed bats from southern Arizona. A significant number of DNA viruses and novel viruses were identified

Bats are a highly diverse mammal species with a dense virome and fascinating immune system. The following project utilizes metagenomics in order to identify DNA viruses present in populations of silver-haired bats and Mexican free-tailed bats from southern Arizona. A significant number of DNA viruses and novel viruses were identified in the Cressdnaviricota phylum and Microvirdae family.

ContributorsHarding, Ciara (Author) / Varsani, Arvind (Thesis director) / Dolby, Greer (Committee member) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Watts College of Public Service & Community Solut (Contributor)
Created2022-05
Description
Wild horses have roamed the Salt River in Mesa, Arizona since the early 1800s and contribute to the great diversity of the region. Conservation of the herd has been a primary focus for many years and a current focus is population stabilization, but little is known about their virome. Circoviridae,

Wild horses have roamed the Salt River in Mesa, Arizona since the early 1800s and contribute to the great diversity of the region. Conservation of the herd has been a primary focus for many years and a current focus is population stabilization, but little is known about their virome. Circoviridae, Genomoviridae, and Smacoviridae are the three Cressdnaviricota viruses that have been identified in horses to date. Smacoviridae is classified by the rolling circle replication-associated proteins (Rep) and has a small (2.3-2.9kb), circular, single-stranded genome. The goal of this study was to identify DNA viruses within the fecal samples of the Salt River horses. Samples were collected along the lower Salt River and analyzed in the lab using a metagenomics approach. There were 422 full novel genomes of smacoviruses detected across all samples that were grouped into 144 species based on the similarity of the pairwise identity. Phylogenetic analysis shows the smacoviruses from this study fall into 3 classified genera and the rest cluster into 11 new clades. These results expand the viral diversity associated with wild horses and Smacoviridae, and further studies are needed to determine the host of these viruses.
ContributorsMcGraw, Hannah (Author) / Varsani, Arvind (Thesis director) / Murphree, Julie (Committee member) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05
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Description
While most household surfactants are biodegradable in aerobic conditions, their presence in a microbiological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in bacteria, such as Pseudomonas aeruginosa. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation

While most household surfactants are biodegradable in aerobic conditions, their presence in a microbiological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in bacteria, such as Pseudomonas aeruginosa. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation of ARG. This study evaluated how the three classes of surfactants affected the microbial community’s structure and ARG in O2-based membrane biofilm reactors (O2-MBfRs) that provided at least 98% surfactant removal. Cationic cetrimonium bromide (CTAB) had by far the strongest impact with highest ARG abundance in the biofilm. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also promoted potential of horizontal gene transfer (HGT) of ARG. Combining results from the metabolome and metagenome identified four possible pathways for CTAB biodegradation. Of special important is a new pathway: β-carbon oxidation of CTAB to produce betaine. An insufficient nitrogen source could lead to irreversible ARB and ARG enrichment in the MBfR biofilm. Finally, a two-stage O2-MBfR successfully removed a high concentration (730 mg/L) of CTAB: Partial CTAB removal in the Lead reactor relieved inhibition in the Lag reactor. Metagenomic analysis also revealed that the Lag reactor was enriched in genes for CTAB and metabolite oxygenation.
ContributorsZheng, Chenwei (Author) / Rittmann, Bruce (Thesis advisor) / Delgado, Anca (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Lai, Yen-Jung (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Metagenomics is the study of the structure and function of microbial communities through the application of the whole-genome shotgun (WGS) sequencing method. Providing high-resolution community profiles at species or even strain levels, metagenomics points to a new direction for microbiome research in understanding microbial gene function, microbial-microbial interactions, and host-microbe

Metagenomics is the study of the structure and function of microbial communities through the application of the whole-genome shotgun (WGS) sequencing method. Providing high-resolution community profiles at species or even strain levels, metagenomics points to a new direction for microbiome research in understanding microbial gene function, microbial-microbial interactions, and host-microbe interactions. My thesis work includes innovation in metagenomic research through the application of ChatGPT in assisting beginning researchers, adopt pre-existed alpha diversity metric for metagenomic data to improve diversity calculation, and the application of metagenomic data in Alzheimer’s disease research.Since the release of ChatGPT in March 2023, the conversation regarding AI in research has promptly been debated. Through the prompted bioinformatic case study, I demonstrate the application of ChatGPT in conducting metagenomic analysis. I constructed and tested a working pipeline aimed at instructing GPT in completing shotgun metagenomic research. The pipeline includes instructions for various essential analytic steps: quality controls, host filtering, read classification, abundance estimation, diversity calculation, and data visualization. The pipeline demonstrated successful completion and reproducible results. Alpha diversity measurement is critical to understanding microbiomes. The widely used Faith’s phylogenetic diversity (PD) metric is agnostic of feature abundance and, therefore, falls short of analyzing metagenomic data. BWPDθ, an abundance weighted variant of Faith’s PD, was implemented in scikit-bio alpha diversity metrics. My analysis shows that BWPDθ does have better performance compared to Faith’s PD, revealing more biological significance, and maintaining their robustness at a lower sampling depth. The progression of Alzheimer’s disease (AD) is known to be associated with alterations in the patient’s gut microbiome. Utilizing metagenomic data from the AlzBiom study, I explored the differential abundance of bacterial pncA genes among healthy and AD participants by age group. The analysis showed that there was no significant difference in pncA abundance between the healthy and AD patients. However, when stratified by age group, within the age group 64 to 69, AD was shown to have significantly lower pncA abundance than the healthy control group. The Pearson's test showed a moderate positive association between age and pncA abundance.
ContributorsXing, Zhu (Author) / Zhu, Qiyun (Thesis advisor) / Lim, Efrem (Committee member) / Snyder-Mackler, Noah (Committee member) / Arizona State University (Publisher)
Created2024
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Description
Peatlands are significant global carbon sinks, where plant litter accumulation outpaces the rate of microbial degradation, which can result in significant emissions of methane and carbon dioxide. The Pastaza-Marañón foreland basin (PMFB) in the western Amazon contains the largest expanse of tropical peatlands in South America, characterized by a diversity

Peatlands are significant global carbon sinks, where plant litter accumulation outpaces the rate of microbial degradation, which can result in significant emissions of methane and carbon dioxide. The Pastaza-Marañón foreland basin (PMFB) in the western Amazon contains the largest expanse of tropical peatlands in South America, characterized by a diversity of soil properties, including pH and mineral concentration. The PMFB is predicted to decrease in its carbon capture capacity along with a rise in greenhouse gas emissions as the climate changes. Therefore, it is imperative to understand the impact that soil properties have on the abundance of functions, microbial physiology, and interspecies interactions between microbial community members. Metagenomic sequencing of soil samples from three geochemically distinct peatlands revealed site-specific enrichment of functions related to carbon, nitrogen, phosphorus, and sulfur cycling. Additionally, 519 metagenome-assembled genomes (MAGs) were recovered, revealing variations in microbial populations responsible for organic matter degradation and nutrient (nitrogen and sulfur) cycling across sites. From these MAGs, a novel family within the Bathyarchaeia was identified, Candidatus Paludivitaceae. This family is putatively capable of carboxydotrophy, able to use CO for energy and biomass. Subsequently they could detoxify the environment of CO benefiting other community members and playing an indirect role in modulating carbon cycling. To experimentally investigate interactions of peatland microbes, co-culture experiments assessed the impact of carbon substrates (4-hydroxybenzoic acid, mannitol, and arginine) on microbial interactions from heterotrophs isolated from two geochemically distinct peatlands. Results indicate substrate and peatland type significantly influence nature and frequency of microbial interactions. The response of microbial genera to carbon substrate also varied showing the role of metabolic traits and substrate preferences in determining growth patterns of microbes. This research advances our understanding of microbial ecology in tropical peatlands and better informs predictions as the climate changes.
ContributorsPavia, Michael Joseph (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Bean, Heather (Committee member) / Bouskill, Nicholas (Committee member) / Penton, Christopher (Committee member) / Arizona State University (Publisher)
Created2024