Human_colon_16S-sc-5035
Human_colon_16S
Cutting-edge transcriptional and bioinformatics approaches will be implemented to assess immune cells at three sites along the healthy adult human colon. Sections will be taken from four sites of the GI tract- caecum, transverse colon, sigmoid colon and oesophagus.  These samples will be collected from cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM) that are representative of healthy tissues since the donors are screened for infections and disease prior to their consideration for donation. Furthermore, medical history of these donors will be available, providing unique accessory information.   The sampling technique will involve incision into the wall of the colon. The mucosa will then be pull through this incision and approximately 2cm x 2cm section of the full thickness of mucosa sampled. The majority of immune cells reside in the lamina propria of the mucosa (Figure 2). Some tissue will be frozen and the remaining digested for single-cell RNA sequencing of immune cells and stromal cells. A swab of the mucosa and the luminal chyme (where appropriate) will also be collected by microbiology culture swabs (in culture gels) and with swabs in PBS. With the help from Professor Trevor Lawley, the diversity of the microbiome will be determined by 16S rRNA sequencing. From these results, changes in diversity of the microbiota and whether this correspond with changes in immune cell heterogeneity will be investigated. If I find major differences in the immune cells or bacteria at these sites than I will ask for more samples to be collect from the next individual.
The human colon contains an extensively diverse microbial ecosystem. The colon immune system interacts closely with this ecosystem, ensuring tolerance in times of 'peace' yet potently reacting against pathogens that cause disease. Studies have highlighted dynamic crosstalk between immune cells and commensals. In particular, germ-free mice colonised with human microbiota have shown at a molecular level (with traditional flow-cytometry) that specific species can induce specific immune cell responses, particularly from T cells (1-4). While studies have demonstrated increasing diversity of microbiota from stomach to stool (5-7), whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown.  The overarching aims of this study are: 1. Create an in-depth reference map of the changing microbiome across healthy human colons. 2. Assess at single-cell resolution T cell and myeloid cell phenotypes within the same colon tissues. 3. Determine whether the changes in microbiome and immune cell profiles with the colon are co-dependent, and demonstrate such relationships, though the intelligent application of human-gnotobiotic mice.