The importance of honey bees in agriculture and the emergence of CCD underscores the need to monitor honey bee associated viruses and microbes in healthy colonies over time. The confinement of Spiroplasma infection to a two-month window demonstrates the value of time-course sampling as opposed to single-collection screens. The development of high throughput platforms, such as the APM, will facilitate monitoring of exogenous agents in order to better understand their effect on honey bee health and survival. Our discovery and genomic characterization of four new viruses will facilitate future monitoring. Temporal characterization of these and the other microbes described herein offers a more complete view of the possible microbe-microbe and microbe-environment interactions. Further studies examining any subtle or combinatorial effects of these novel microbes are required to understand their role in colony health. Increased analysis of prospectively collected samples is essential to address the hypothesis that either one or more viruses and/or microbes cause CCD. To our knowledge, this is the first U.S. honey bee pathogen monitoring study to report both comprehensive pathogen incidence and relative abundance of specific pathogens over time. Results from our molecular analysis pipeline (APM, PCR, qPCR, ultra deep sequencing) provide a basis for future epidemiologic studies aimed at determining the causes of CCD. . Honey bees colonies were periodically supplemented with sugar syrup and protein supplement. In April (1 gallon) and October (2 gallons) bees were fed 50% (weight/volume) sucrose; in November all colonies received 3 gallons of a 1:1 mixture of high fructose corn syrup-55 (HFCS-55, 55% fructose, 42% glucose) and sucrose syrup. Additional sugar syrup was given to colonies based on colony weight (,80 lbs -3 gallons, 80-90 lbs -2 gallons., 90-100 lbs -none). This operation experienced an average 18% colony loss from November 2009 to February 2010. Colonies with younger queens (#2 years old) experienced 11% loss, whereas colonies with older queens experience 21% loss.