We collected 19 colon content samples from wild-type and new AD models (AppNL-G-F rats) at 3 and 12 months of age and profiled the composition and functionality of gut microbiota using multi-omics approaches. Using the newly emerged proteomics method, data-independent acquisition (DIA), integrated with a sample-matched database, we detected the significantly differentially expressed microbial proteins and observed the functional alterations of gut microbiota at gene ontology (GO), Enzyme Commission (EC) and Clusters of orthologous groups (COG) levels. Our multi-omics study provided a more detailed comprehensive picture of the dynamic gut microbiota at the over-all molecular level.