Browsing by Subject "microbiome"
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Item Comparison of the Bacterial Gut Microbiome of North American Triatoma spp. With and Without Trypanosoma cruzi(Frontiers Media S.A., 2020-03-13) Mann, Allison E.; Mitchell, Elizabeth A.; Zhang, Yan; Curtis-Robles, Rachel; Thapa, Santosh; Hamer, Sarah A.; Allen, Michael S.Chagas disease, caused by the hemoflagellate protist Trypanosoma cruzi, affects nearly 6 million people worldwide, mainly in Latin America. Hematophagous triatomine insects ("kissing bugs") are the primary vectors of T. cruzi throughout the Americas and feed on a variety of animals, including humans. Control of triatomines is central to the control of T. cruzi infection. Recent advances in mitigation of other insect-borne diseases via the manipulation of insect-associated bacteria as a way to halt or slow disease transmission has opened questions to the applicability of these methods to Chagas disease vectors. Few studies have examined the hindgut microbiome of triatomines found in North America. In the current study, two species of triatomines were collected across Texas, United States, screened for the presence of T. cruzi, and analyzed for the bacterial composition of their hindguts using a 16S rRNA gene-fragment metabarcoding approach. We compared diversity of microbial community profiles across 74 triatomine insects to address the hypothesis that the richness and abundance of bacterial groups differ by T. cruzi infection and strain type, blood meal engorgement status, insect species, sex, and collection location. The gut microbial community of individual triatomines was characterized by low intraindividual taxonomic diversity and high interindividual variation that was weakly predicted by triatomine species, and was not predicted by triatomine sex, collection location, T. cruzi infection status, or blood meal score. However, we did find bacterial groups enriched in T. cruzi-positive individuals, including Enterobacterales, and Petrimonas. Additionally, we detected Salmonella enterica subspecies diarizonae in three triatomine individuals; this species is commonly associated with reptiles and domesticated animals and is a pathogen of humans. These data suggest that Triatoma spp. in Texas have variable patterns of colonized and transient bacteria, and may aid in development of novel means to interfere with transmission of the Chagas disease parasite T. cruzi. Deeper understanding of the effects of parasite infection on diverse insect vector microbiomes may highlight disease transmission risk and facilitate discovery of possible intervention strategies for biological control of this emerging vector-borne disease of global health significance.Item DEEP SEQUENCING OF CULTIVATION-NEGATIVE BRONCHOAVEOLAR LAVAGE SAMPLES FROM MECHANICALLY VENTILATED TRAUMA PATIENTS REVEALS DEFICITS IN TRADITIONAL CLINICAL PROTOCOLS(2014-03) Smith, Ashley D.; Zhang, Yan; DeSpain, Kevin; Huebinger, Ryan M.; Allen, Michael S.Patients undergoing mechanical ventilation are at risk for infections such as ventilator-acquired pneumonia. Standard clinical protocols call for pathogen screening on culture plates which can only detect a limited number of bacteria. We sampled the lungs of mechanically ventilated trauma patients, and by using molecular-based deep sequencing techniques we found several potentially pathogenic bacteria in samples that traditional techniques labeled as “no growth” or normal “respiratory tract flora." Purpose (a): Bronchoaveolar lavage (BAL) is a method of screening mechanically ventilated patients for potentially pathogenic microogranisms. Traditional culture-based techniques used in clinical laboratories detect a limited number of known bacteria; consequently, some samples may be falsely reported as “cultivation-negative” or possessing only “normal respiratory tract flora.” To ascertain the potential for false negative results, we performed next generation DNA sequencing on BAL samples previously determined to be “cultivation negative” or “respiratory tract flora” by standard plate methods. Methods (b): Nine samples were taken from mechanically ventilated trauma patients in the Surgical Intensive Care Unit (SICU) subjected to BAL as part of the standard of care. DNA was extracted from the samples and the 16S rRNA subunit was amplified and sequenced using the Ion Torrent Personal Genome Machine. Sequences were analyzed using Mothur data-analysis pipeline to identify the appropriate taxonomic designation. Results (c): Results indicated that the majority (>77%) were dominated by a single organism. One third (3/9) of the samples analyzed were dominated by Neisseria spp. Other potential pathogens found to be dominant within the BAL samples included Streptococcus, Haemophilus, Aeromonas, and Rothia spp. Contamination from the oral cavity were also likely in two samples as evidenced by the identification of Porphyromonas and Prevotella spp. Conclusions (d): Our study demonstrates potential benefits of using next-generation sequencing to supplement the current culture-dependent clinical diagnostic methods. The knowledge gained from analyzing the lung microbiome of “culture-negative” and “respiratory tract flora” may be an important tool for identifying difficult to cultivate species associated with lung infections in mechanically ventilated patients.Item Effects of a Synthetic Amino Acid Diet: Insights from the Guy Microbiome, Inflammation, and Behavior(2021-05) Mancilla, Viviana J.; Allen, Michael S.; Jones, Harlan P.; Phillips, Nicole R.; Planz, John V.; Ellis, DorettePhenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet and frequently supplemented with an amino acid formula to maintain proper nutrition. PKU patients often report high levels of anxiety along with symptoms of gastrointestinal distress (i.e., chronic diarrhea, constipation, cramps); symptoms previously associated with gut microbiome dysbiosis. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. The gut microbiome is a collection of microbes residing primarily in the large intestine. The colon is a major production site for short chain fatty acids (SCFAs) through anaerobic fermentation by commensal bacteria. SCFAs provide a source of energy for the colonocytes, as well as provide anti-inflammatory benefits. The production of SCFA appears to be dependent on the availability of soluble fibers and members of the gut microbiota capable of fermentation. We characterized the gut microbiome of adults with PKU for the first time and identified signs of dysbiosis. We then focused on the synthetic, low fiber, nature of the amino acid diet in a murine model. In this interdisciplinary study, we monitored the effect of a consuming synthetic diet on the composition of the murine gut microbiome over the course of 13 weeks, beginning at weaning. At the conclusion of the feeding period, mice we observed for anxiolytic behavior, locomotion, and cognition. We also searched for markers of inflammation through colon shrinkage, changes in cytokine levels within several tissues, and determined the concentration of SCFAs in the colon at the conclusion of the feeding period. The gut microbiome of mice fed the synthetic diet experienced significant deviation from the control group which affected relative abundance of beneficial bacteria. Mice on the synthetic diet were found to have shorter colons, lower concentration of SCFAs in the colon, and demonstrated elevated exploratory behavior.Item Effects of temperature on bacterial microbiome composition in Ixodes scapularis ticks(John Wiley & Sons, Inc., 2018-09-21) Thapa, Santosh; Zhang, Yan; Allen, Michael S.Ixodes scapularis, the blacklegged deer tick, is the principal vector of Lyme disease in North America. Environmental factors are known to influence regional and seasonal incidence of Lyme disease and possibly the endemicity of the disease to the northeastern and upper mid-western regions of the United States. With a goal to understand the impact of environmental temperature on microbial communities within the tick, we investigated the bacterial microbiome of colony-reared I. scapularis ticks statically incubated at different temperatures (4, 20, 30, and 37°C) at a constant humidity in a controlled laboratory setting by comparison of sequenced amplicons of the bacterial 16S V4 rRNA gene to that of the untreated baseline controls. The microbiomes of colony-reared I. scapularis males were distinct than that of females, which were entirely dominated by Rickettsia. In silico removal of Rickettsia sequences from female data revealed the underlying bacterial community, which is consistent in complexity with those seen among male ticks. The bacterial community composition of these ticks changes upon incubation at 30°C for a week and 37°C for more than 5 days. Moreover, the male ticks incubated at 30 and 37°C exhibited significantly different bacterial diversity compared to the initial baseline microbiome, and the change in bacterial diversity was dependent upon duration of exposure. Rickettsia-free data revealed a significantly different bacterial diversity in female ticks incubated at 37°C compared to that of 4 and 20°C treatments. These results provide experimental evidence that environmental temperature can impact the tick bacterial microbiome in a laboratory setting.Item Examining the skin and workplace microbiome following the return to the University of North Texas Health Science Center after self-isolation(2021-08) Khichi, Ophelia J.; Allen, Michael S.; Zhang, Yan; Zascavage, Roxanne R.; Rosales, ArmandoThe human skin microbiome contains trillions of microbiomes that colonize the human body. It is unknown how social distancing and an increase in handwashing due to the COVID-19 pandemic affect the bacterial communities that reside on the human hands & fomites. In this research, bacterial swabs from individual's dominant hand, forearm of their dominant hand, and a fomite from the workplace environment were taken, and the resident microflora, i.e., the skin microbiome, was investigated. The DNA from the samples were extracted and amplified by PCR. Samples were then pooled for sequencing of the V4 region of the 16S ribosomal RNA gene using Illumina's MiSeq platform and subsequently analyzed for community composition. The results were compared against each other to determine how an individual and a fomite's microbiome shifted following their return to work. Furthermore, the results were used to determine if individual's microbiome became more similar to each other as they returned to work in the same building.Item The Adult Phenylketonuria (PKU) Gut Microbiome(MDPI, 2021-03-04) Mancilla, Viviana J.; Mann, Allison E.; Zhang, Yan; Allen, Michael S.Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formula to maintain proper nutrition. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 region of the 16S rRNA gene from stool samples collected from adults with PKU (n = 11) and non-PKU controls (n = 21). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria. Gut community diversity was lower in PKU individuals, though this effect was only statistically suggestive. A total of 65 genera across 5 phyla were statistically differentially abundant between PKU and control samples (p < 0.001). Additionally, we identified six metabolic pathways that differed between groups (p < 0.05), with four enriched in PKU samples and two in controls. While the child PKU gut microbiome has been previously investigated, this is the first study to explore the gut microbiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKU adults and highlights the need for further studies to understand the effects of dietary restrictions.Item The effects of temperature on the microbiome of the ectoparasite Amblyomma americanum(2016-12-01) Willis, Kelsi R.; Michael AllenTicks are the second leading vector of disease transmission to humans. Though observations of the bacteria carried by ticks started almost a century ago there are still unanswered questions, not least among those being ‘what external factors shape the composition of bacteria within the tick’. The answer to this question is integral to our understanding of the viability and virulence of the diseases ticks carry, and may have implications on how to control them and limit their transmission. There are many instances where distribution of diseases carried by ectoparasites do not mimic the vector’s habitat range, and given that there has been little research looking specifically at external effects on the microbiome of ticks, we proposed to investigate if temperature influenced the microbiome composition of the ectoparasite A. americanum under controlled laboratory conditions. We hypothesized that there would be statistically significant differences among the bacterial community compositions within the microbiomes of A. americanum based on the incubation temperature. In order to test this, colony-reared ticks were exposed to environments with several different incubation temperatures for 15 or 30-days. DNA was then collected and sequenced from these ticks and subsequent metagenomic analysis was conducted to investigate the bacterial composition of their microbiomes. Results indicated that there was no significant difference in microbial communities with respect to temperature, but there was in terms of length of incubation.