Browsing College of Computer, Mathematical & Natural Sciences by Subject "16S rRNA"
Now showing 1 - 4 of 4
Results Per Page
- ItemLongitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection(Springer Nature, 2016-07-08) Morris, Alison; Paulson, Joseph N.; Talukder, Hisham; Tipton, Laura; Kling, Heather; Cui, Lijia; Fitch, Adam; Pop, Mihai; Norris, Karen A.; Ghedin, ElodieLongitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease. Cynomolgous macaques were infected with the SIV-HIV chimeric virus SHIV89.6P. Bronchoalveolar lavage fluid samples were collected pre-infection and every 4 weeks for 53 weeks post-infection. The microbiota was characterized at each time point by 16S ribosomal RNA (rRNA) sequencing. We observed individual variation in the composition of the lung microbiota with a proportion of the macaques having Tropheryma whipplei as the dominant organism in their lungs. Bacterial communities varied over time both within and between animals, but there did not appear to be a systematic alteration due to SHIV infection. Development of obstructive lung disease in the SHIV-infected animals was characterized by a relative increase in abundance of oral anaerobes. Network analysis further identified a difference in community composition that accompanied the development of obstructive disease with negative correlations between members of the obstructed and non-obstructed groups. This emphasizes how species shifts can impact multiple other species, potentially resulting in disease. This study is the first to investigate the dynamics of the lung microbiota over time and in response to immunosuppression in a non-human primate model. The persistence of oral bacteria in the lung and their association with obstruction suggest a potential role in pathogenesis. The lung microbiome in the non-human primate is a valuable tool for examining the impact of the lung microbiome in human health and disease.
- ItemNovel Methods for Metagenomic Analysis(2010) White, James Robert; Pop, Mihai; Applied Mathematics and Scientific Computation; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)By sampling the genetic content of microbes at the nucleotide level, metagenomics has rapidly established itself as the standard in characterizing the taxonomic diversity and functional capacity of microbial populations throughout nature. The decreasing cost of sequencing technologies and the simultaneous increase of throughput per run has given scientists the ability to deeply sample highly diverse communities on a reasonable budget. The Human Microbiome Project is representative of the flood of sequence data that will arrive in the coming years. Despite these advancements, there remains the significant challenge of analyzing massive metagenomic datasets to make appropriate biological conclusions. This dissertation is a collection of novel methods developed for improved analysis of metagenomic data: (1) We begin with Figaro, a statistical algorithm that quickly and accurately infers and trims vector sequence from large Sanger-based read sets without prior knowledge of the vector used in library construction. (2) Next, we perform a rigorous evaluation of methodologies used to cluster environmental 16S rRNA sequences into species-level operational taxonomic units, and discover that many published studies utilize highly stringent parameters, resulting in overestimation of microbial diversity. (3) To assist in comparative metagenomics studies, we have created Metastats, a robust statistical methodology for comparing large-scale clinical datasets with up to thousands of subjects. Given a collection of annotated metagenomic features (e.g. taxa, COGs, or pathways), Metastats determines which features are differentially abundant between two populations. (4) Finally, we report on a new methodology that employs the generalized Lotka-Volterra model to infer microbe-microbe interactions from longitudinal 16S rRNA data. It is our hope that these methods will enhance standard metagenomic analysis techniques to provide better insight into the human microbiome and microbial communities throughout our world. To assist metagenomics researchers and those developing methods, all software described in this thesis is open-source and available online.
- ItemThe role of dehalorespiring bacteria in the reductive dechlorination of polychlorinated biphenyls in Baltimore harbor sediment microcosms(2007-03-29) Fagervold, Sonja Kristine; Sowers, Kevin R; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Baltimore Harbor sediment microcosms were incubated with the 12 most predominant congeners in Aroclor 1260 and their intermediate products to identify the major dechlorination pathways. Most congeners were dechlorinated in the meta position, although some dechlorination in the para and ortho positions was observed. The major dechlorination products were tetrachlorinated biphenyls with unflanked chlorines. Specific dechlorination rates of parent and intermediate PCB congeners were determined to identify the rate limiting reactions. To identify the microorganisms responsible for the dechlorination pathways, I developed PCR primers specific for the 16S rRNA genes of known PCB dehalogenating bacteria. These PCR primers were used in conjunction with DGGE to selectively identify the microorganisms that catalyzed each dechlorination reaction. Only three phylotypes were identified that catalyze the dechlorination of Aroclor 1260, and the selective activities of these phylotypes were determined. Phylotype DEH10 had high sequence similarity to Dehalococcoides spp., while phylotype SF1 had high sequence similarity to the o-17/DF-1 group of PCB dechlorinating bacteria. The third phylotype had 100% sequence similarity to the ortho-dechlorinating bacterium o-17 described previously from Baltimore Harbor sediments. Most dechlorination reactions for all three phylotypes were growth-linked, indicating that PCB-impacted environments have the potential to sustain populations of PCB dechlorinating organisms. To investigate whether bioaugmentation would be feasible for bioremediation of PCB contaminated sites, Baltimore Harbor sediment microcosms were supplemented with known dechlorinators and their effects on PCBs dechlorination patterns determined. The addition of different dechlorinators resulted in different dechlorination patterns. Finally, novel putative reductive dehalogenases were identified from the PCB dechlorinating bacterium DF-1 using degenerate PCR primers. Comparative sequence analyses indicated that they had high sequence similarity to both confirmed and putative dehalogenases from several Dehalococcoides species. In conclusion, microorganisms that can dechlorinate Aroclor 1260 have been identified for the first time and dechlorination of congener mixtures was shown to occur by the growth-linked complementary activities of bacterial consortia within the Chloroflexi. Demonstration that bioaugmentation with these organisms can influence rates and pathways of dechlorination, combined with the development of molecular assay for monitoring their fate, provide potentially valuable tools for the development of bioremedial strategies for PCB contaminated sediments.
- ItemSTUDIES OF PERIPHYTIC ALGAE ON ALGAL TURF SCRUBBERSTM ALONG THE CHESAPEAKE BAY: COMMUNITY STRUCTURE, SYSTEMATICS, AND INFLUENCING FACTORS(2012) Laughinghouse, Haywood Dail; Kangas, Patrick C; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This is an ecological and systematic study of periphytic algae growing in an ecologically-engineered system used for water quality improvement: the Algal Turf Scrubber or ATSTM. This technology consists of an attached algal community growing on screens in a shallow floway through which water is pumped. The study was conducted on small-scale, experimental floways at three sites within the Chesapeake Bay watershed: on the Susquehanna River in southeastern Pennsylvania (freshwater) and on the Great Wicomico and York Rivers in Virginia (brackish water). A total of 330 taxa were identified at the sites from 2008-2011. The majority of taxa at all three sites belonged to the phylum Bacillariophyta, but a large number of taxa from Chlorophyta and, to a lesser degree, Cyanobacteria were also found at the freshwater site. Algae found in the ATSTM exhibited a diversity of life forms and modes of attachment within the community. Although these system appear to be dominated by a "canopy" of attached, filamentous species, more than half of the total abundance (cell density) were solitary, unattached taxa that grow as an "understory" within the three dimensional structure of the community. Longitudinal patterns were examined on the longest floways (90 m long) at the freshwater site. The community nutrient uptake rate (mass of nitrogen or phosphorus m-2 day-1) for the harvested algal biomass was found to decline from the top to the bottom of the floway for a system constructed at 2% slope but no distinct pattern was found for a system constructed at 1% slope. The majority of algal taxa were evenly distributed along the floway from top to the bottom, in terms of frequency of occurrence, suggesting a general lack of longitudinal specialization within the community. A detailed review of the systematics of the Order Oscillatoriales (Cyanobacteria) found on the ATSTM was undertaken since this group has not been studied much in the Chesapeake Bay watershed. Twenty-four taxa were examined, described morphologically and their nomenclature reviewed. Comparing 16s rRNA gene analyses of planktonic and periphytic Pseudanabaena, it was suggested that periphytic Pseudanabaena be revised and elevated to a new genus, Ilyonema.