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Highlights d Antibiotics perturb the metabolic capacity of the murine gut microbiome d Amoxicillin elevates expression of starch utilization genes in B. thetaiotaomicron d Fiber supplementation protects B. thetaiotaomicron from amoxicillin in vitro d Host diet has a major effect on the response of the microbiome to amoxicillin

SUMMARYThe importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.