The aim of this thesis is to describe symbiotic gastrointestinal bacterial populations in relation to their environment, both at the community and cellular level, in order to advance the field of microbial ecology. Two different levels of relations are examined: in bacterial populations as they undergo differentiation, and in bacterial symbiotic communities in relations with a host. Bacterial populations routinely collaborate in order to fully differentiate in response to environmental stress. The literature review herein describes the current state of knowledge about bacterial programmed cell death during differentiation. This study found that programmed lysis of the Low G+C Gram positive bacterial symbiont Epulopisciumoccurs after marked DNA replication in the terminally differentiated mother cell, as well as the expected replication in developing offspring cells. This energetically expensive process sustains the large metabolically active cell and may allow nutrient storage in the form of DNA for later use by the offspring or host. The close relative of Epulopiscium, Metabacterium polyspora, has different DNA dynamicsand reproduces through the formation of multiple dormant endospores. In model systems DNA replication is blocked after induction of sporulation, In contrast, M. polysporareplicates DNA inside developing forespores. This may allow M. polysporato modulate the number of forespores produced based on local nutrient availability within the gastrointestinal tract of its host. Both Epulopiscium and M. polysporaappear to have evolved reproductive strategies and related DNA replication dynamics that are suited to their particular relationship with the host. Studies of the gastrointestinal microbiota of the coral reef fish Pomacanthus sexstriatus also illustrate the ability of organisms to shape and be shaped by their environment. The unusual prevalence of sulfate reducing bacteria in this community could aid host digestion of a wider range of algae, including those that use sulfonated carbohydrates as a defense against predation. This ability may have an impact on larger coral reef ecology, promoting coral reef resilience by controlling fast-growing algal populations. In summary, investigations into these bacterial populations and communities provide data that can only be explained when bacteria are placed within the context of their environment and evolutionary history.