Abstract
Summary The gastrointestinal tract of mammals is inhabited by several hundred bacterial species. While the effects of the gut microbiota upon the host have been widely studied, the microbial response to host factors has only recently attracted attention. In order to investigate the influence of the host on the physiology of gastrointestinal bacteria, a simplified model of host–bacteria interaction was created by associating germfree mice with commensal Escherichia coli . Here we demonstrate the feasibility of analysing the bacterial response to the conditions in the digestive system by a proteomics‐based approach. Two‐dimensional gel electrophoresis (2D‐GE) followed by electrospray ionization‐tandem mass spectrometry (ESI‐MS/MS) was used to identify bacterial proteins from caecal and faecal samples. In a set of 60 arbitrarily chosen spots of stably and differentially expressed proteins, 50 different bacterial proteins were identified. Their ascribed functions suggest that the host‐associated bacteria adapt their metabolism to the conditions in the intestine by utilizing arginine, asparagine and aspartate as well as glucose/galactose, ribose, maltose, glucuronate, galacturonate and gluconate as substrates. Thirteen proteins not previously detected on 2D‐gels and 10 proteins with unknown or poorly characterized physiological function were identified, while the existence of three proteins had so far only been inferred from predictions or by homology.