Alfredo Blakeley-Ruiz

Also known as: Alfredo

Microbiome, Proteomics, Genomics, Systems Biology

Works (10)

Updated: March 31st, 2025 10:45

2025 article

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

PROTEOMICS, Vol. 2.

By: A. Bartlett n, J. Blakeley-Ruiz  n, T. Richie  n, C. Theriot n & M. Kleiner n 

topics (OpenAlex): Gut microbiota and health; Probiotics and Fermented Foods; Nutritional Studies and Diet
Sources: NC State University Libraries, Web Of Science
Added: March 3, 2025

2024 article

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

Rajczewski, A. T., Blakeley-Ruiz, J. A., Meyer, A., Vintila, S., McIlvin, M. R., Bossche, T. V. D., … Jagtap, P. D. (2024, September 22).

By: A. Rajczewski, J. Blakeley-Ruiz, A. Meyer, S. Vintila, M. McIlvin, T. Bossche, B. Searle, T. Griffin ...

topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Metabolomics and Mass Spectrometry Studies
Source: ORCID
Added: October 1, 2024

2024 article

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

Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2024, June 27).

By: A. Awan  n, A. Bartlett *, J. Blakeley-Ruiz  n, T. Richie *, C. Theriot  n & M. Kleiner n 

topics (OpenAlex): Gut microbiota and health; Muscle metabolism and nutrition; Probiotics and Fermented Foods
Source: ORCID
Added: July 1, 2024

2024 article

Dietary protein source strongly alters gut microbiota composition and function

Blakeley-Ruiz, J. A., Bartlett, A., McMillan, A., Awan, A., Walsh, M. V., Meyerhoffer, A., … Kleiner, M. (2024, April 5).

By: J. Blakeley-Ruiz  n, A. Bartlett *, A. McMillan  n, A. Awan  n, M. Walsh, A. Meyerhoffer  n, S. Vintila  n, J. Maier n  ...

topics (OpenAlex): Gut microbiota and health; Probiotics and Fermented Foods; Nutritional Studies and Diet
Source: ORCID
Added: July 22, 2024

2023 article

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2023, December 7).

By: A. Bartlett  n, A. Blakeley-Ruiz n , T. Richie  n, C. Theriot  n & M. Kleiner n 

topics (OpenAlex): Gut microbiota and health; Probiotics and Fermented Foods; Nutritional Studies and Diet
TL;DR: Large quantities of microbial DNA and protein are found in casein-based diets, which highlight the necessity of evaluating diet samples in diet-microbiota studies to ensure that potential microbial content of the diet can be accounted for in microbiome measurements. (via Semantic Scholar)
Source: ORCID
Added: December 8, 2023

2022 journal article

Considerations for constructing a protein sequence database for metaproteomics

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20, 937–952.

By: J. Blakeley-Ruiz  n & M. Kleiner n 

Contributors: J. Blakeley-Ruiz  n

author keywords: Metaproteome; Metagenomics; Microbiome; Microbial community; Multi-omics; Microbiota; Microbial ecology
topics (OpenAlex): Advanced Proteomics Techniques and Applications; Mass Spectrometry Techniques and Applications; Genomics and Phylogenetic Studies
TL;DR: An overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies is provided, and a decision tree and best practices for choosing and implementing database construction strategies are provided. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 25, 2022

2022 journal article

Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice

ISME Communications, 2(1).

By: J. Blakeley-Ruiz *, C. McClintock*, H. Shrestha *, S. Poudel *, Z. Yang*, R. Giannone *, J. Choo, M. Podar * ...

Contributors: J. Blakeley-Ruiz *

topics (OpenAlex): Gut microbiota and health; Diet and metabolism studies; Tryptophan and brain disorders
TL;DR: Investigating the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome. (via Semantic Scholar)
Source: ORCID
Added: August 25, 2022

2020 thesis

Extracting detailed metabolic information and connections from mammalian gut microbiomes via metaproteomics

(PhD diss., University of Tennessee). https://trace.tennessee.edu/utk_graddiss/6194

By: J. Blakeley-Ruiz

Contributors: J. Blakeley-Ruiz

trace.tennessee.edu
Source: ORCID
Added: August 25, 2022

2019 journal article

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences.

Alfredo Blakeley-Ruiz

topics (OpenAlex): Gut microbiota and health; Neuroendocrine regulation and behavior; Diet and metabolism studies
TL;DR: This commentary extends their review of microbiota-gut-brain literature by highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research. (via Semantic Scholar)
Source: ORCID
Added: August 25, 2022

2019 journal article

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes

Microbiome.

Alfredo Blakeley-Ruiz

author keywords: Gut microbiome; Metaproteomics; Crohn's disease; Longitudinal analyses; Microbial metabolic function; Human microbiome
MeSH headings : Acetylglucosamine / analysis; Adult; Bacteria / genetics; Bacteria / metabolism; Crohn Disease / microbiology; Crohn Disease / surgery; Cytidine Monophosphate N-Acetylneuraminic Acid / analysis; Fatty Acids, Volatile / analysis; Feces / microbiology; Female; Gastrointestinal Microbiome / genetics; Gastrointestinal Microbiome / physiology; Humans; Male; Middle Aged; Proteome / metabolism; Proteomics; RNA, Ribosomal, 16S / genetics
topics (OpenAlex): Gut microbiota and health; Epigenetics and DNA Methylation; Pancreatic and Hepatic Oncology Research
TL;DR: Examining metaproteomes measured in several Crohn’s disease patients’ post-resection surgery across the course of 1 year suggests that microbial membership composition may not be the best way to characterize a phenotype and suggests it seems to be more informative to examine and characterize the functional composition of a gut microbiome. (via Semantic Scholar)
Source: ORCID
Added: August 25, 2022

Employment

Updated: August 26th, 2020 16:40

2020 - present

North Carolina State University Raleigh, NC, US
Postdoc Plant and Microbial Biology

2011 - 2014

Infectious Disease Research Institute Seattle, WA, US
Research Assitant TB Discovery

Education

Updated: August 26th, 2020 16:39

2014 - 2020

University of Tennessee Knoxville, TN, US
PhD Genome Science and Technology

2007 - 2011

University of Notre Dame Notre Dame, IN, US
B.S. Biological Sciences

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