Medicine and Health Sciences Commons^™

Characterization Of Microbial Communities In The Mammary Glands And The Influence Of This Microbiota On Health And Disease, Camilla Urbaniak

Electronic Thesis and Dissertation Repository

The collective microbes and their genomic activity within us, referred to as the human microbiome, is crucial in maintaining health, and disruptions in composition and activity have been associated with various diseases. Considering the importance of breast milk in neonatal development and the high rate of breast cancer in women, the objective of my thesis was to obtain a comprehensive analysis of the microbiota of the mammary glands and to examine the influence of these organisms on health and disease.

Human milk is an important source of bacteria for the developing infant. While a variety of studies over the last …

Unifying The Analysis Of High-Throughput Sequencing Datasets: Characterizing Rna-Seq, 16s Rrna Gene Sequencing And Selective Growth Experiments By Compositional Data Analysis., Andrew D Fernandes, Jennifer Ns Reid, Jean M Macklaim, Thomas A Mcmurrough, David R Edgell, Gregory B Gloor

Biology Publications

BACKGROUND: Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis …