The health of animals, including humans, is dependent on their resident microbiota, but the complexity
of the microbial communities makes these associations difficult to study in most animals. Exceptionally,
the microbiology of the pea aphid Acyrthosiphon pisum is dominated by a single bacterium Buchnera
aphidicola (B. aphidicola). A 1H NMR-based metabonomic strategy was applied to investigate metabolic
profiles of aphids fed on a low essential amino acid diet and treated by antibiotic to eliminate B.
aphidicola. In addition, differential gel electrophoresis (DIGE) with mass spectrometry was utilized to
determine the alterations of proteins induced by these treatments. We found that these perturbations
resulted in significant changes to the abundance of 15 metabolites and 238 proteins. Ten (67%) of the
metabolites with altered abundance were amino acids, with nonessential amino acids increased and
essential amino acids decreased by both perturbations. Over-represented proteins in the perturbed
treatments included catabolic enzymes with roles in amino acid degradation and glycolysis, various
cuticular proteins, and a C-type lectin and regucalcin with candidate defensive roles. This analysis
demonstrates the central role of essential amino acid production in the relationship and identifies
candidate proteins and processes underpinning the function and persistence of the association