The Plan

In this project I will use publically available data to

  1. estimate the functional composition of a “normal” bee gut microbiome
  2. assemble in silico communties of bee gut strains
  3. estimate how well designed communities recapitulate natural microbiomes

Datasets

I used three published sets of metagenomes from:

  1. T. Regan, M. W. Barnett, D. R. Laetsch, S. J. Bush, D. Wragg, G. E. Budge, F. Highet, B. Dainat, J. R. de Miranda, M. Watson, M. Blaxter, T. C. Freeman, Characterisation of the British honey bee metagenome. Nat. Commun. 9, 4995 (2018).
  2. P. Engel, V. G. Martinson, N. A. Moran, Functional diversity within the simple gut microbiota of the honey bee. Proc. Natl. Acad. Sci. U. S. A. 109, 11002–11007 (2012).
  3. K. M. Ellegaard, P. Engel, Genomic diversity landscape of the honey bee gut microbiota. Nature Communications. 10 (2019).

I downloaded isolate genomes from the NCBI Assembly database, computationally annotated some metadata through entrez, and then manually added additional metadata (host species).

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