Every mammalian cell in the body contains a timekeeper – a molecular clock that tracks time-of-day information. It is well-established that interactions between central (SCN) and peripheral oscillators can influence the mammalian circadian rhythms in physiology and behavior. These experiments examine how the environment influences circadian rhythms in both behavior and physiology. Chapter 3 tests the hypothesis that the gut microbiota is a component of the circadian network by chronotyping mice born and reared devoid of bacteria (germ free mice) and comparing those to ‘normal’ SPF mice. Chapter 4 examines the role of gut microbiota in mediating the effects of high fat diet on circadian rhythms by chronotyping both bacterially replete and germ free mice fed either a normal chow or high fat diet. Chapter 5 examines the influence of gestational sickness on circadian rhythms in mice with different gut microbiota composition, using a mouse model of maternal immune activation in mice obtained from different rodent vendors known for their differential presence of gut microbiota species. Chapter 6 examines interacting timescales that generate seasonal rhythms in immune function. Seasonally breeding rodents, Siberian hamsters (Phodopus sungorus) were immune challenged every three hours of the circadian cycle in both winterlike and summerlike photocycles. Chapter 6 examines both innate and adaptive immune traits and how seasonal and daily timescales interact to produce rhythmic changes in immune function. Together, these experiments explore transkingdom interactions and their influence on host behavior.