The human gastrointestinal tract is one of the most densely populated ecosystems on Earth, with a concentration of 10^13 – 10^14 bacterial cells per gram of fecal matter in the large intestine. They may be commensal, symbiotic, or pathogenic in relation to the host and are distributed nearly equally into two major phyla – the Bacteroides and the Firmicutes. These bacteria and their associated phage contribute immensely to human health and disease states. Obesity, diabetes, Crohn’s disease, metabolism, immunity, and even mood are associated with specific microbiota. Changes in community composition away from steady state can lead to dysbiosis and disease. Temperate prophage integrated into bacterial genomes propagate by duplicating their genetic material whenever their host does, until specific signals induce the lysogen to form phage particles and lyse the host cell. Foods and chemicals consumed by humans are likely to trigger these signals, thereby modulating gut community compositions and human physiology. Here I examine the effects of over 130 commonly consumed chemical additives, foods, and plant extracts on the growth and prophage induction capacity of bacterial species representing the two major phyla of the gut. This examination is preceded by the development of two novel experimental techniques – one to mass-analyze bacterial growth curves, and another to quantify induced prophage with flow cytometry. These studies showed that the tested compounds differentially affect bacterial growth, and likely human gut community composition. Several new prophage inducing agents were also identified – including Stevia rebaudiana and bee propolis extracts. These methods and results present novel tools toward the eventual manipulation of the human gut microbiome.