Browsing by Subject "Microbiota"
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Item Bacterial microbiomes of Ixodes scapularis ticks collected from Massachusetts and Texas, USA(BioMed Central Ltd., 2019-06-24) Thapa, Santosh; Zhang, Yan; Allen, Michael S.BACKGROUND: The blacklegged tick, Ixodes scapularis, is the primary vector of the Lyme disease spirochete Borrelia burgdorferi in North America. Though the tick is found across the eastern United States, Lyme disease is endemic to the northeast and upper midwest and rare or absent in the southern portion of the vector's range. In an effort to better understand the tick microbiome from diverse geographic and climatic regions, we analysed the bacterial community of 115 I. scapularis adults collected from vegetation in Texas and Massachusetts, representing extreme ends of the vector's range, by massively parallel sequencing of the 16S V4 rRNA gene. In addition, 7 female I. scapularis collected from dogs in Texas were included in the study. RESULTS: Male I. scapularis ticks had a more diverse bacterial microbiome in comparison to the female ticks. Rickettsia spp. dominated the microbiomes of field-collected female I. scapularis from both regions, as well as half of the males from Texas. In addition, the male and female ticks captured from Massachusetts contained high proportions of the pathogens Anaplasma and Borrelia, as well as the arthropod endosymbiont Wolbachia. None of these were found in libraries generated from ticks collected in Texas. Pseudomonas, Acinetobacter and Mycobacterium were significantly differently abundant (p < 0.05) between the male ticks from Massachusetts and Texas. Anaplasma and Borrelia were found in 15 and 63% of the 62 Massachusetts ticks, respectively, with a co-infection rate of 11%. Female ticks collected from Texas dogs were particularly diverse, and contained several genera including Rickettsia, Pseudomonas, Bradyrhizobium, Sediminibacterium, and Ralstonia. CONCLUSIONS: Our results indicate that the bacterial microbiomes of I. scapularis ticks vary by sex and geography, with significantly more diversity in male microbiomes compared to females. We found that sex plays a larger role than geography in shaping the composition/diversity of the I. scapularis microbiome, but that geography affects what additional taxa are represented (beyond Rickettsia) and whether pathogens are found. Furthermore, recent feeding may have a role in shaping the tick microbiome, as evident from a more complex bacterial community in female ticks from dogs compared to the wild-caught questing females. These findings may provide further insight into the differences in the ability of the ticks to acquire, maintain and transmit pathogens. Future studies on possible causes and consequences of these differences will shed additional light on tick microbiome biology and vector competence.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 Improving Human Identification Using the Human Skin Microbiome(2021-12) Sherier, Allison J.; Budowle, Bruce; Leudtke, Robert; Phillips, Nicole R.There are times when biological evidence has too low of quality or quantity of human DNA to provide enough information for human identification (HID). However, nucleic acids from the human skin microbiome are sources of genetic material that may be useful for HID. The studies in this dissertation test the hypothesis that specific single nucleotide polymorphisms (SNPs) of selected human skin microorganisms can be used to attribute an unknown microbiome sample to an individual. The first study investigated how Wright's fixation index (FST) can be used to select potentially informative SNPs for HID. SNPs with high estimated FST were ascertained in three different ways to examine three distinct hypotheses. The hypotheses focused on testing whether a high FST, increased taxonomic abundance, and/or using a predetermined panel would be the most effective for HID. Classification accuracies ranged from 88 – 95%, and the method using the most taxa possible performed the best. Results from the study support that using genetic distance to select informative markers from the human skin microbiome for HID was viable. The predetermined panel only achieved an 88% accuracy, although it would be the most applicable of the tested method for forensic case work. The second study focused on using FST estimations to select SNPs abundant in 51 individuals sampled at three body sites in triplicate for HID. The most common SNPs (present in ≥ 75% of the samples) which had FST estimates ≥ 0.1 were used with least absolute shrinkage and selection operator (LASSO) to select a list of informative SNPs for HID. The final list (i.e., hidSkinPlex+) contains 365 SNPs and achieved a 95% classification accuracy on 459 samples. The hidSkinPlex+ lays the foundation for a targeted sequencing panel that can be used to further study the stability and specificity of human skin microorganism SNPs for HID applications.Item Patient genetics is linked to chronic wound microbiome composition and healing(PLOS, 2020-06-18) Tipton, Craig D.; Wolcott, Randall D.; Sanford, Nicholas E.; Miller, Clint; Pathak, Gita A.; Silzer, Talisa K.; Sun, Jie; Fleming, Derek; Rumbaugh, Kendra P.; Little, Todd D.; Phillips, Nicole; Phillips, Caleb D.The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.Item Use of ATCC[R] MSA-2002[TM] for Validation of Extraction and Amplification Techniques in 16S Microbial Community Profiling(2018-05) Foley, Brianna A.; Allen, Michael; Warren, Joseph; Zhang, Yan; Maddux, Scott D.The implementation of microbiome analysis is an emerging area of focus in forensic research. However, microbiome analysis is not well validated for use in forensic analyses and there is no standard protocol in place. In this research a comprehensive analysis of extraction and amplification techniques employed during investigation of microbial communities was performed using ATCC[R] MSA-2002[TM] as a mock microbial community. Comparison of DNA extraction protocols was performed followed by an analysis of commercially-available polymerases. Samples were pooled for sequencing of the V4 region of 16S ribosomal RNA gene using the Illumina MiSeq System, and subsequently analyzed for community composition. The results were compared with the known genomic data of the mock microbial community and statistical methods were employed to determine the extent of deviation.Item Variations of the lung microbiome and immune response in mechanically ventilated surgical patients(PLOS, 2018-10-24) Huebinger, Ryan M.; Smith, Ashley D.; Zhang, Yan; Monson, Nancy L.; Ireland, Sara J.; Barber, Robert C.; Kubasiak, John C.; Minshall, Christian T.; Minei, Joseph P.; Wolf, Steven E.; Allen, Michael S.Mechanically ventilated surgical patients have a variety of bacterial flora that are often undetectable by traditional culture methods. The source of infection in many of these patients remains unclear. To address this clinical problem, the microbiome profile and host inflammatory response in bronchoalveolar lavage samples from the surgical intensive care unit were examined relative to clinical pathology diagnoses. The hypothesis was tested that clinical diagnosis of respiratory tract flora were similar to culture positive lavage samples in both microbiome and inflammatory profile. Bronchoalveolar lavage samples were collected in the surgical intensive care unit as standard of care for intubated individuals with a clinical pulmonary infection score of >6 or who were expected to be intubated for >48 hours. Cytokine analysis was conducted with the Bioplex Pro Human Th17 cytokine panel. The microbiome of the samples was sequenced for the 16S rRNA region using the Ion Torrent. Microbiome diversity analysis showed the culture-positive samples had the lowest levels of diversity and culture negative with the highest based upon the Shannon-Wiener index (culture positive: 0.77 ± 0.36, respiratory tract flora: 2.06 ± 0.73, culture negative: 3.97 ± 0.65). Culture-negative samples were not dominated by a single bacterial genera. Lavages classified as respiratory tract flora were more similar to the culture-positive in the microbiome profile. A comparison of cytokine expression between groups showed increased levels of cytokines (IFN-g, IL-17F, IL-1B, IL-31, TNF-a) in culture-positive and respiratory tract flora groups. Culture-positive samples exhibited a more robust immune response and reduced diversity of bacterial genera. Lower cytokine levels in culture-negative samples, despite a greater number of bacterial species, suggest a resident nonpathogenic bacterial community may be indicative of a normal pulmonary environment. Respiratory tract flora samples were most similar to the culture-positive samples and may warrant classification as culture-positive when considering clinical treatment.