The human body is home to a diverse ecosystem of trillions of bacteria. In fact, your digestive tract alone — including your small and large intestine — houses about 99% of your entire microbiome. In fact, the human body has more microbes than human cells. Some of these bacteria can make you sick, but the overwhelming majority are important for keeping you healthy and fending off infections. Sometimes, the same bacteria can do both. Recently, scientists began studying the correlation between the health of the gut microecosystem, and other health issues, and found that gut bacteria are closely tied to other aspects of health. The american gut microbiome project used over 11,000 16s rRNA samples from people across the United States in their analyses.
Phenotypic attributes and geolocation allowed for examination of the association between the human microbiome and external environmental factors like age, race, diet, and place of residence. The American gut microbiome project has fecal, oral, skin, and other body site samples collected from thousands of participants. From this large database, a subset of patient samples was selected. Each sample included several types of samples: gut, mouth, or skin and were then run on the following pipeline for mapping and production of abundance tables.
This pipeline includes two algorithms. The first is a tool for aligning sequencing reads onto long reference sequences that is ultrafast and memory efficient. Bowtie 2 is often the first step in pipelines for comparative genomics including ChIP-seq, BS-seq, and RNA-seq, and metagenomics as it aligns sequences to a reference genome, in this case, a database of bacterial genomes. The second is the poscount algorithm was developed by Tauber Center. PosCount yields a table of abundances (for each sample) for each repeat that was mapped on repetitive elements.
This project is currently undergoing and we hope to release an educational set of lessons soon.