Biology subjects

Blakeley-Ruiz, J.

Publications and source records attributed to Blakeley-Ruiz, J..

3 recordsLinked to original sources

bioRxiv2025

Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota

Dietary protein source differentially impacts long-term health outcomes, yet the specific host responses underlying these health effects remain unclear, including which are direct effects of protein source and which are microbiota-mediated. Using metagenome-informed metaproteomics, we determined that protein source altered the abundance of host proteins related to proteolysis, immunity, and the gut barrier as well as microbial function in mice. These stool host responses further reflected site-specific responses throughout the intestinal tract. Additionally, while some host responses were microbiota-dependent, others were microbiota-independent. These effects of dietary protein source on the host and microbiota translated to humans. Notably, microbial enzymes related to mucin degradation increased consistently in response to egg white protein in both mice and humans. Our results show that protein source impacts multiple aspects of host physiology through microbiota-dependent and independent routes, providing essential insights into mechanisms underpinning protein source-driven differences in health outcomes.

microbiology↗

bioRxiv2024

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being Data-Dependent Acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-Independent Acquisition Mass Spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.

systems biology↗

bioRxiv2024

Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota

Protein is an essential macronutrient and variations in its source and quantity have been shown to impact long-term health outcomes. Differential health impacts of dietary proteins from various sources are likely driven by differences in their digestibility by the host and subsequent availability to the intestinal microbiota. However, our current understanding regarding the fate of dietary proteins from different sources in the gut, specifically how component proteins within these sources interact with the host and the gut microbiota, is limited. To determine which dietary proteins are efficiently digested by the host, and which proteins escape host digestion and are used by the gut microbiota, we used high-resolution mass spectrometry to quantify proteins that constitute different dietary protein sources before and after digestion in germ-free and conventionally raised mice. We detected proteins from all sources in fecal samples of both germ-free and conventional mice suggesting that even protein sources with high digestive efficiency make it to the colon where they can serve as metabolic substrate for gut microbiota. Additionally, we found that specific component proteins of dietary protein sources were degraded to a greater extent in the presence of the microbiota. We found that specific proteins with functions that could potentially impact host health and physiology were differentially enriched in germ-free or conventionally raised mice. These findings reveal large differences in the fate of dietary protein from various sources in the gut which could explain some of their differential health impacts.

microbiology↗