Christina asks
> "A survey of the microbial communities of CCD hives" How did they do the survey?

Reply, quoted:

> We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by the examination of samples collected from several sites over a period of 3 years. 

> Total RNA was extracted to capture RNA viruses as well as other pathogens. The RNA was pooled as presumed CCD-positive, presumed CCD-negative, and royal jelly for pyrosequencing. The raw sequencing reads were trimmed and assembled into contiguous sequences (contigs). Analysis using nucleotide-nucleotide BLAST (BLASTN) and BLASTX (8) revealed the presence of bacteria, fungi, parasites, metazoa, and viruses. Bacterial analysis indicated community composition (Table 1) similar to that in samples collected in Africa, Switzerland, and Germany, suggesting that A. mellifera has similar bacterial flora worldwide. 

> The gut lumen contains the majority of microorganisms in most insects. Because a similar profile of bacterial types was found in dissected intestines from A. mellifera, the bacterial species described here probably represent a characteristic gut-inhabiting community. Although we cannot exclude that a strain of a normally commensal bacterium has become pathogenic while retaining a near-identical 16S rRNA sequence, we observed no clear shift in abundance to suggest that this occurred in CCD. A trend toward increased abundance of one of the Gammaproteobacterial taxa in the CCD bees may reflect physiological changes accompanying CCD and affecting the commensal community.

-- Diana L. Cox-Foster et al. Science 318, 283 (2007)

> Since CCD colonies have a marked deficit of older workers, age structure per se could well contribute to the bacterial pattern observed.

-- Cornman RS, Tarpy DR, Chen Y, Jeffreys L, Lopez D, et al. (2012) Pathogen Webs in Collapsing Honey Bee Colonies. PLoS ONE 7(8): e43562. doi:10.1371/ journal.pone.0043562

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