Human microbiomes are increasingly seen as a key to understanding human biology, whether it be in studying health/disease or in documenting human diversity. Anthropological interest in human microbiomes has primarily focused on inventorying shifts microbial abundance between lifestyles and over time. While undoubtedly valuable information, these taxonomic inventories lack application of theoretical frameworks that can provide a deeper understanding of human-microbiome interactions. In my work, I integrate microbiome data with ideas typically used in the study of macroecological systems. I present a background on ecological frameworks and their general applicability to human microbiome studies in Chapter 1. In Chapters 2-4, I present unique research on human microbiome ecology. Chapter 2 is a first-of-its-kind study on ecological dynamics in ancient human microbiomes, in which I demonstrate how network analysis can inform on general microbiome community structure in ancient coprolites and dental calculus, as well as demonstrate overlap in key ecological signatures between ancient and contemporary non-industrial populations. Chapter 3 is a demonstration of the value of interrogating potential microbiome stability and resilience in a specific niche, namely short-chain fatty acid (SCFA) production. Our research indicates that non-industrial gut microbiomes are more resilient for SCFA production and industrial SCFAs are encoded by a few, closely related species. These results come in the face of substantial database bias that inhibits study of non-industrial gut microbiomes. Finally, Chapter 4 describes vaginal and gut microbiomes in women with Ovarian Cancer (OC). We determine that women with OC have lower than expected vaginal Lactobacillii dominance, which creates ecological space for an opportunistic bacteria such as Escherichia, to thrive in women who suffer quick recurrence of cancerous growth after platinum chemotherapy.