TABLE 2 

Major challenges for bee microbiome studies

Area of studyQuestions and considerations
1. Defining bee healthWhat are the best measures of fitness at the individual and colony levels? In social insects, fitness experiments with individual bees may not reflect the fitness of a colony.
2. Microbiome compositionHow do distinct microbes interact to affect hosts? Microbes likely influence one another’s effect on the host. Coinfections pose a challenge for disentangling individual roles, and certain experiments may need to be conducted in microbiome-free hosts.
3. Host geneticsBees are genetically diverse, which may affect microbiome-host interactions. Can the influence of genetic differences among hosts be controlled for?
4. Environmental factorsThese are likely to contribute to microbiome composition and function. How can such environmental factors be reliably measured and tested?
5. Physiological variablesThe physiology and development of bees can differ substantially according to season, age, housing, and nutrition. Do these differences influence microbiome relationships?
6. Microbiome quantificationDifferent diagnostic tools (quantitative and qualitative) exist to study microbiome compositions. How comparable are these tools?
7. Wild pollinatorsFor the majority of the ~20,000 wild bee species, the microbiome composition and functions are unknown. Systematic and standardized sampling approaches are needed.
8. Data accessibilitySystematic archiving of large sequencing datasets with accompanying metadata information is crucial so that cross-study analyses can be conducted.