Will be describing perturbations, e.g. antibiotics and disease Describing 2007 clindamycin study, Jernberg et al 2007 ISMEJ. Long term impact of antibiotic use. One clone of bacteriodes that dominates community, resistant to antiboitics. Cites Jernberg et al 2010 microbiology. - Erick Matsen

Crohn's disease. Swedish twin cohort. Healthy twin pairs, those having UC, and Crohn's. Looking at microbiome, metagenome, meta-transcriptome, meta-proteome, and meta-metabolome. 16s data. See differentiation between UC, Ileal CD, and Colonic CD. A major difference between Faecalibacterium prausnitzii. Metaproteomics. Can also see functions differentiating. Get bacterial proteins and human proteins that differentiate between disease. Map onto pathways. Jansson et al PLoS ONE 2009. See 1000s of metabolites that differentiate. - Erick Matsen

Restoration from a perturbed state? Can we restore? C. diff fecal transplant story. Profile her community before and after. Before treatment, very strange community. The recipient very closely matches donor's profile. Cure! Idea of alternate stable states and basins of attraction. - Erick Matsen