Palaeogenetic research on human pathogenic and microbiomic bacteria has been largely restricted to bloodborne pathogens from skeletal tissue and, due to short lengths of degraded ancient DNA, small-scale single loci studies. My thesis has expanded the breadth and depth of palaeomicrobial knowledge via the study of novel specimen types with next-generation technologies. Presented in sandwich thesis format, I discuss genome-scale studies of three previously-unstudied historical pathogens: 19th century Vibrio cholerae (cholera) from an alcohol-preserved intestine from Philadelphia, and medieval Staphylococcus saprophyticus (urinary tract infections) and Gardnerella vaginalis (bacterial vaginosis) from calcified urogenital infections of a Trojan woman. Cholera persists as a dangerous modern disease that was also responsible for severe historic epidemics. My research confirms that 19th century pandemics were caused by an O1 classical strain that may have possessed genomic features that contributed increased virulence. S. saprophyticus and G. vaginalis are opportunistic pathogens of the urogenital microbiome, especially in reproductive-age females. Using very high endogenous DNA content of the calcified infections, I have reconstructed one of the most complete ancient bacterial genomes for S. saprophyticus and coding genome for G. vaginalis. Both ancient pathogens possess most of the virulence and urogenital adaptive genes of modern strains, indicating similar ecological roles for these species in past female health. Finally, I successfully use LLMDA microarray technology (never before utilized for ancient DNA research) to detect ancient pathogens. LLMDA provides an inexpensive and informative alternative to high-throughput sequencing for assessing the metagenomic content of ancient samples. Together, my findings provide a framework emphasizing the need to broadly study past microbiomes in conjunction with specific pathogens. Using molecular data, this work supports anthropological views of infectious disease ecology related to the first epidemiological transition and historical narratives. Taken together with the recent literature on ancient pathogen genomes, my findings indicate that palaeogenome sequences may not necessarily reveal any specific signatures of greater virulence, and interpretations of past diseases must necessarily take into account additional host, environmental, and cultural factors. / Thesis / Doctor of Philosophy (PhD)