The manuscript
Alfredo and his co-workers applied an integrated metagenomics-metaproteomics approach to show that different dietary protein sources altered the composition and function of the gut microbiome of mice fed defined-diets with different dietary protein sources. The most pronounced effects on the composition of the microbiome were observed with diets containing yeast or egg white proteins, which led to an expansion of Bacteroides thetaiotamicron at the expense of bacteria of the order Clostridia. Along with the increased abundance of B. thetaiotamicron, the authors observed an increase in various glycoside hydrolases from polysaccharide utilization loci (PULs) associated with yeast mannoprotein degradation in case of the yeast diet group and degradation of mucins in case of the egg white diet group. Remarkably, these proteome adaptations could be reproduced in vitro by growing B. thetaiotamicron in media prepared from the dietary protein sources, providing further evidence that B. thetaiotamicron thrives on yeast and egg white diets in vivo by utilizing glycosylated proteins.
The manuscript underlines the fact that not only fiber and fat significantly influence the composition and function of the microbiome, but also the protein source in the diet. In addition, the authors show very well how well metaproteomics signatures can be reproduced in vitro, which significantly increases the informative value.
The author
Dr. J. Alfredo Blakeley-Ruiz is a postdoctoral fellow at North Carolina State University in Raleigh, North Carolina, USA. Alfredo operates at the interface between genome science, analytical chemistry, and microbiology to understand gut microbiota function. His current research explores interactions between host, diet, and gut microbes that increase susceptibility to disease.
After getting a B.S. in biology from the University of Notre Dame, Alfredo spent three years working on tuberculosis drug discovery before pursuing a Ph.D. in the Genome Science and Technology program jointly sponsored by the University of Tennessee, Knoxville, and Oak Ridge National Laboratory. In his dissertation, he used metaproteomics to uncover metabolic functions related to disease and health in animal gut microbiomes, including humans. Alfredo graduated in 2020 and joined the lab of Dr. Manuel Kleiner at North Carolina State University for a postdoc. In addition to his postdoctoral research on the effect of dietary protein on the gut microbiota, he is also pursuing multiple international collaborations investigating how to improve metaproteomic methods and applying omics research to bioplastics degradation. Alfredo’s postdoc was funded for two years by a NIH T32 fellowship from the Center for Gastrointestinal Biology and Disease (CGIBD) at the University of North Carolina at Chapel Hill. He has since received additional funding from CGIBD to investigate the role of dietary protein on susceptibility to inflammation in mouse models of colitis and is currently pursuing funding to investigate humanized models of IBD.
Alfredo is actively seeking to establish his own lab at a university or research organization. His lab will investigate the interface between diet, microbiomes, and human health.
