Technical Abstract: Honey bee colonies have innumerable symbiotic bacteria and fungi that are essential to the health of the colony. In the first part of this series, we discussed the importance of microbes in maintaining the health of honey bee colonies. The bacteria, yeasts and molds that live in a healthy colony and in the bees themselves are needed for food processing and digestion and help control the growth of pathogens. Part-2 of this series provides information on factors that might affect the number and diversity of microbes in a colony. These include genetics of the bees, pollen types, anitbiotic treatments to control colony diseases, exposure to fungicides, and supplemental feeding with protein supplements and high fructose corn syrup. A discussion on how microbes might contribute to the phenotypic differences in lines of bees especially in population growth is included.