Colorectal cancer (CRC) has a 5-year survival rate of 68% yet it still has a mortality rate of 50,000 per year. While CRC has a host of causes, one that stands out is TGFβ deficient signaling, which is disrupted in a majority of high-microsatellite-instability or inflammation-associated CRCs. Since TGFβ is a multifunctional cytokine, it has been elusive to determine whether its effect on cancer development is operating through inflammation, differentiation or developmental pathways. Additionally, it is now becoming apparent that a great number of CRC cases can be associated with and possibly caused by gut bacteria dysbiosis. Here, I present a metagenomic and metatranscriptomic study of the interactions between TGFβ deficient signaling, inflammatory signaling, and the microbiome in a CRC mouse model. TGFβ deficient mice have reduced amounts of Firmicutes as well as mRNA counts of a key butyrate enzyme. Lack of butyrate, as shown by previous literature, could be inhibiting apoptosis and promoting growth. Also, TGFβ deficient mice have increased mRNA counts of polyamine producing genes, which could act synergistically with butyrate reduction. I find that H. hepaticus inoculation, as a source of inflammatory signaling, affects another species, M. schaedleri, to produce pro- inflammatory lipopolysaccharides. Additionally, H. hepaticus itself has increased oxidative phosphorylation; reactive oxygen species from this process could be adding to cancer-promoting DNA damage. Taken together, TGFβ deficient signaling and H. hepaticus inoculation, disrupt enough pathways to cross the threshold of carcinogenicity in 40% of the mice in our study. The results of this study emphasize the importance of microbiome function and represent possible new avenues of treatment.

Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman's rank correlation [r(s)] = >0.81; false-discovery rate [q] = <= 0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Diverse and abundant coral associated microbial communities may play a key role in coral resistance to and recovery from unwavering stressors currently threatening coral reefs worldwide. The composition and structure of the coral microbiome is integral to coral health as microbes can play beneficial (e.g. nutritional or protective) or negative (e.g. pathogenic or opportunistic) roles in the coral. To review the impacts of stressors on the coral microbiome, I compiled data from 39 studies, each tracking microbial community shifts in corals experiencing stress from climate change, pollution or overfishing. Stress was associated with shifts in coral microbial communities. I found that regardless of stressor, microbial alpha diversity increased under stress, with Vibrionales, Flavobacteriales and Rhodobacterales commonly found on stressed corals, and Oceanospirillales not as abundant on stressed corals. In addition, I used 16S rRNA sequencing to evaluate how local and global stressors affect the community structure of the coral microbiome for the two coral species, Porites lobata and Montipora foliosa. I monitored tagged coral colonies at two human disturbance levels (i.e. high and low), before and during a thermal bleaching hotspot at Kiritimati, Kiribati. Human disturbance, a bleaching hotspot, and coral species were all important drivers of coral microbiome community structure. My results suggest that human disturbance increases microbial alpha and beta diversity, although results vary between coral species, with P. lobata having more of a difference between disturbance levels. Similarly, bleaching increased beta diversity at low disturbance sites. Both human disturbance and thermal stress appeared to homogenize coral microbiomes between species and thermal stress appeared to homogenize communities between disturbance levels. Thus, both human disturbance and bleaching appear to stress the coral and destabilize its microbiome. However, intense thermal stress (i.e. 12.86 DHWs) appears to have a greater influence than human disturbance, probably due to corals responding to stressful conditions in a similar manner. In conclusion, my results highlight the impact of local and global stressors on coral microbiome community structure. / Graduate / 2018-04-26 / 0359

Viral respiratory infections (VRI) are common in children with cystic fibrosis (CF) and are associated with significant clinical deterioration. Little previous research has been conducted on VRI in adults with CF. This thesis describes a prospective study to determine the epidemiology and clinical impact of VRI among 100 adults with CF.The incidence of identifiable VRI was 1.66 cases/patient-year. Rhinovirus accounted for 72.5% of viruses. Identifiable VRI was associated with increased risk of pulmonary exacerbation, increased respiratory symptoms and higher C-reactive protein levels. Changes in the climate and seasons affected the incidence of identifiable VRI. Rhinovirus was most common in autumn and other viruses predominated during winter. Warmer ambient temperatures were associated with increased risk of rhinovirus infection while other viruses were more common in colder temperatures. Genetic sequencing of a subset of 42 rhinoviruses identified during the study showed that rhinovirus A accounted for 69% of cases and was associated with more severe respiratory symptoms and higher C-reactive protein levels than rhinovirus B.The impact of identifiable VRI on changes to bacterial communities within the lungs of patients with CF was investigated. Ribosomal intergenic spacer analysis (RISA) was developed as a tool to profile the bacterial diversity of CF sputum and was compared with standard culture and 16S rRNA gene pyrosequencing. No consistent effect of identifiable VRI on the microbial diversity of CF sputum was detected with any of these methods in longitudinal analysis of a subset of 18 patients.

Nitrification is currently the most common means of ammonia removal from wastewaters in temperate climates. In conventional suspended growth systems operating in northern climate regions, nitrification completely ceases at temperatures below 8°C. This is a considerable concern in passive treatment systems where wastewater temperatures can reach as low as 1°C for extended periods in the winter months. There is evidence biofilm technologies have the ability to nitrify at low temperatures, however, the literature is missing an understanding of low temperature nitrification and the subsequent impacts during seasonal changes. Additionally, there is an urgent need to gain a fundamental knowledge of the interplay between nitrifying performance optimization, biofilm morphology and the microbiome. This research aims to fill these needs using nitrifying moving bed biofilm reactors (MBBRs) at the lab and pilot scale. This research concluded the most important factor determining MBBR carrier selection is a combination of surface area and pore space size. Although high surface area to volume carriers are attractive, the propensity to clog at high loading rates significantly decreases the removal rates. The viability of the biomass and ammonia oxidizing bacterial communities were not significantly changed, indicating the ammonia removal rates were reduced due to loss of surface area in the clogged carriers. Operation at 1°C demonstrated significant rates of nitrification can be attained and stable for extended periods of operation. This study developed the first kinetic curve at 1°C with a maximum removal rate of 0.35 gN/m2·d. The performance of the post carbon removal nitrifying MBBR systems were shown to be enhanced at 1°C by an increase in the viable embedded biomass as well as thicker biofilm. This effectively increased the number of viable cells present during low temperature operation, which partially compensated for the significant decrease in rate of ammonia removal per nitrifying cell. At all studied loading rates at 1°C, the ammonia oxidizing bacteria were primarily in the family Nitrosomonadaceae (greater than 95 percent abundance of AOB population) and the nitrite oxidizing bacteria were primarily the genus Nitrospira (greater than 99 percent abundance of NOB population). Operation at 20°C demonstrated high rates of removal in high loaded condition and robustness in extreme low loaded conditions. In both high loaded and extreme low loaded conditions the viability of the nitrifying biomass was sustained, with the family Nitrosomonadaceae as the primary ammonia oxidizing bacteria and the genus Nitrospira as the primary nitrite oxidizing bacteria. In extreme low loaded conditions and as well during start-up phases there are high prevalence of bacteria not directly related to the nitrification process. Their presence however indicates a dynamic process with changes in microbial composition within the biofilm matrix in response to varying conditions. Change in microbial composition likely helps stabilize and maintain the biofilm matrix enhancing process robustness in the temperate climates. The new knowledge gained in this research optimizes the operation of nitrifying MBBR systems and elucidates the impacts of operational conditions on the biofilm and microbial community of nitrifying MBBR systems to further our understanding of nitrifying attached growth treatment technologies. The results of this study are anticipated to be used to design the first MBBR treatment system for year round ammonia removal in passive treatment systems located in northern climate regions.

Background During the first stages of development human infants are either fed human milk or human milk substitutes (infant formulas). The composition of infant formulas and human milk differ drastically, including a difference in protein constituents and bacterial load. Due to the high global frequency of infant formula use, the humanization of infant formulas to better reflect the complex nature of human milk is warranted. To better understand the role of human milk components, the fate and function of a key bacterial sensor in human milk, soluble CD14, was determined. Additionally, the microbiome of human milk was analyzed from a metagenomic standpoint in an attempt to determine which types of bacteria are present in human milk and what their potential biological function might be. Results In rodent models, ingested sCD14 persisted in the gastrointestinal tract and was transferred intact into the blood stream. Once transferred to the blood, ingested sCD14 retained its ability to recognize lipopolysaccharide and initiate an immune response in pups. This transfer of sCD14 across the epithelial barrier was also observed in human cells in vitro, where it appears to be dependent on Toll-like receptor 4. Using Illumina sequencing and the MG-RAST pipeline, the human milk metagenome of ten mothers was sequenced. DNA from human milk aligned to over 360 prokaryotic genera, and contained 30,128 open reading frames assigned to various functional categories. The DNA from human milk was also found to harbor immune-modulatory DNA motifs that may play a significant role in immune development of the infant. Conclusions Given the complex nature of human milk in comparison to its bovine or plant based substitutes, the results presented in this thesis warrant future modification of infant formulas to include non-nutritive bioactive components. Current human milk components not yet present in infant formulas include the diverse microbiome of human milk, the immune-modulatory DNAs which those microbes harbor, and bioactive human proteins such as sCD14.

With recent research being conducted in categorizing and analyzing the human microbiome, evidence has now linked the human microbiome to a range of diseases. Dysbiosis of the human gut microbiome exists in colon cancer, obesity, and Clostridium difficile infections. The use of fecal microbiota transplants has been proven effective in treating recurrent C.difficile infections by restoring gut microbiota. More needs to be done to establish fecal microbiota transplants procedures, effectiveness, and safety. Once established, fecal microbiota transplants may play a role in modulating other diseases linked to human gut microbiome dysbiosis.

Atmospheric aerosols have been studied in great depth in regards to its metrological and chemical characterizations. Covering about 33% of the planet, the Global Dust Belt is the major source of wind-blown dust. Airborne aerosols play important roles in the Earth systems, impacting the marine and terrestrial ecosystems, human and organismal health. Aerosolized dust can carry a diverse range of microorganisms that may be transported across large distances. If surviving the transport, influence, as vectors supporting microbial populations or as pathogens to other organisms, the recipient ecosystems where they may be delivered through dry and wet depositions. Located in the middle of the global dust belt area, the Red Sea receives about 1.2 Mt of emitted dust particles per storm and a total of 6 Mt dust deposition from the annual 5-6 storm events, which may contain important loads of microorganisms. This dissertation characterizes the taxonomical compositions of airborne prokaryotes and micro-eukaryotes and their transport history in the dust-associated microbiome, and the functional profile of the airborne microorganisms. The samples required to achieve these goals were collected with a high-volume dust collector over the Red Sea from the coastal and offshore regions over two years. In addition, microbial communities sampled from the surface Red Sea water were used to establish the possible relationship, suggesting an exchange, between the airborne microbial communities and those in the Red Sea. Since relying on culture5 based analyses would take no notice of unculturable microorganism, culture-independent techniques were followed to detect the vast majority of the biological particles on the sampled air filters. However, large volumes of air should be collected due to the difficulty of acquiring enough genomic materials from the low density of airborne microorganisms for molecular assays. Sahara Deserts and deserts in the Arabian Peninsula represented the major sources of microbial inputs to the Red Sea atmosphere. Hence, a high number of allergens, plant and mammalian pathogens, human and animal parasites have been detected in airborne dust samples, which could be of concern. Functionally, dust-associated microbiome has exclusive lifestyle’s features that facilitate a resilient strategy to survive during airborne transportation, so-called “aeolian lifestyle.”

The human gut microbiome is a vast ecosystem of microorganisms that play an important role in human metabolism, immunological function, and even inflammatory gut diseases. Metagenomics research on the human gut microbiome has demonstrated the presence of DNA from dietary yeast species like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected in metagenomics studies is solely from dead dietary sources or if they can live and colonize the human gut like their close relative Candida albicans. While S. cerevisiae can adapt to low oxygen and acidic environments, it has yet to be explored whether it can metabolize mucin, the primary carbon source found in the mucus layer of the human gut. Mucins are large, gel-forming, highly glycosylated proteins that make up a majority of carbohydrate sources in the gut mucosa. This work determined that S. cerevisiae can utilize mucin as their main carbon source which results in a significant reduction in cell size. Additionally, an aspartyl protease named Yps7, part of a family containing known homologues to mucin-degrading C. albicans proteins in S. cerevisiae, is important for growth on mucin media. To further identify biological pathways required to grow optimally in mucin, both a transcriptome analysis on wild type cells (BY4743) and a chemogenomics screen was performed. In total, 2131 genes demonstrated significant differential expression in mucin media, and 30 genes upon their deletion impacted their growth on mucin. Both these screens suggest that mitochondrial function is required for proper growth in mucin, which was further elucidated by the change in mitochondrial morphology and oxygen consumption in yeast cells upon mucin treatment. Indeed, the uncharacterized open reading frame YCR095W-A is required for growth on mucin as the deletion mutant showed dysfunction in mitochondrial morphology and cellular respiration, further suggesting a potential role in mitochondrial function. Importantly, this project serves as the initial step towards establishing if our most common dietary fungus can survive in the mucus environment of the human gut.

Recent works has highlighted the contribution of microbes to animal function. In this regard, the microbial community associated with corals has become a growing field of research in order to understand how microbes contribute to the host organisms’ response to environmental changes. It has been shown that microbes associated with corals have important functions in the coral holobiont such as immunity and nutrient assimilation. However, corals are notoriously difficult to work with. To this end, the sea anemone Aiptasia is becoming a model organism for coral symbiosis. Given the importance of host-­microbiome interactions, the topic of this thesis is to assess microbial structure of Aiptasia, culture prominent bacterial members, and compare bacterial community structure to corals. Different molecular methods have been applied using 16S rRNA bacterial gene fragments to characterize the microbial composition of Aiptasia. 16S rRNA gene sequence derived from cultured bacteria was compared to 16S rRNA gene sequences retrieved from native Red Sea Aiptasia. Inter-­individual as well as methodological differences were found to account for variance in microbiome composition. However, all approaches showed a highly abundant microbial taxon belonging to the genus Alteromonas in all samples. The Alteromonas species was successfully isolated for further research targeting microbiome selection mechanisms in Aiptasia. Future investigations by using different molecular tools will help to define the functions and relationship between the Aiptasia and its complex microbiome.