Article Figures & Data
- FIG 1
A resource and analysis platform for bee microbiome studies. Large amounts of sequence data, metadata, and methods are being generated by different research groups around the globe. A centralized platform is needed to systematically archive such information, to make it available to other researchers in the field, to allow cross-study analyses, and to standardize approaches. The bee microbiome platform will enable more detailed analyses of available data to formulate novel hypotheses about bee health and microbiome evolution.
- TABLE 1
Outstanding questions in bee microbiome research
Field of knowledge Research question Bee health 1. How do different microbes impact bee health? a. Nutritional versus defensive symbioses? b. Host range and fitness effects of pathogens? 2. Which combinations of microbes are most detrimental or beneficial? 3. Do microbes in wild and managed bee populations influence health in similar ways? 4. How do environmental factors influence host-microbiome interactions? 5. How do the interactions among microbiome members modulate the impact of individual members, to the benefit or cost to the host? Evolution and ecology 1. What are the functions of the different microbes in the bee gut? 2. Which factors drive the composition and evolution of the bee microbiome? 3. How does the social/solitary lifestyle of bees influence microbiome evolution? 4. How has domestication changed the bee microbiome? - TABLE 2
Major challenges for bee microbiome studies
Area of study Questions and considerations 1. Defining bee health What 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 composition How 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 genetics Bees are genetically diverse, which may affect microbiome-host interactions. Can the influence of genetic differences among hosts be controlled for? 4. Environmental factors These are likely to contribute to microbiome composition and function. How can such environmental factors be reliably measured and tested? 5. Physiological variables The physiology and development of bees can differ substantially according to season, age, housing, and nutrition. Do these differences influence microbiome relationships? 6. Microbiome quantification Different diagnostic tools (quantitative and qualitative) exist to study microbiome compositions. How comparable are these tools? 7. Wild pollinators For 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 accessibility Systematic archiving of large sequencing datasets with accompanying metadata information is crucial so that cross-study analyses can be conducted. - TABLE 3
Practical steps for advancements
Challenge and step 1. Many microbes are important to bee biology, but often an experiment focuses on only one type. Simultaneous screening for 16S rRNA genes, 18S rRNA genes, and viruses is needed to yield a more comprehensive picture of the microbiome. 2. If simultaneous screening as proposed in step 1 is not feasible, archiving aliquots of DNA/RNA/whole samples will facilitate future identification of the other microbes. 3. Quantitative PCR of total individual (i.e., per bee) microbial loads will help with the interpretation of relative compositional data, as typically acquired by amplicon sequencing. 4. Proper metadata are needed for interpretation and comparison of results. As much information as possible should be recorded and made accessible for an experiment. 5. Standardized experimental bee lines should be established to control for host genetic differences between laboratories. 6. Standardization of protocols, such as the methods of isolation of host, bacterial, and viral DNA/RNA, is necessary for cross-study analysis. 7. Sampling and sequencing environmental sources, such as flowers and nest components, will help to understand the spread and transmission of bee microbes. 8. Bee microbiome researchers should be engaged to actively participate in the bee microbiome project and to help establish this necessary and important community service.
Supplemental Material
Table S1
Comprehensive overview of Apis bee diseases, including known hosts and known effects on hosts. Table S1, XLSX file, 0.02 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S2
Comprehensive overview of Apis bee microbes. Table S2, XLSX file, 0.01 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S3
Comprehensive overview of non-Apis bee microorganisms. Table S3, XLSX file, 0.02 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Text S1
Literature support for the Apis bee diseases. Download Text S1, DOCX file, 0.02 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Text S2
Literature support for the Apis bee microbes. Download Text S2, PDF file, 0.1 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Text S3
Literature support for the non-Apis bee microorganisms. Download Text S3, DOCX file, 0.02 MB.
Copyright © 2016 Engel et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Additional Files
Supplementary Data
Supplementary Data
- Text s1, DOCX - Text s1, DOCX
- Text s2, PDF - Text s2, PDF
- Text s3, DOCX - Text s3, DOCX
- Table st1, XLSX - Table st1, XLSX
- Table st2, XLSX - Table st2, XLSX
- Table st3, XLSX - Table st3, XLSX
