@article{bartlett_blakeley-ruiz_richie_theriot_kleiner_2023, title={Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies}, url={http://dx.doi.org/10.1101/2023.12.07.570621}, DOI={10.1101/2023.12.07.570621}, abstractNote={Abstract}, author={Bartlett, Alexandria and Blakeley-Ruiz, Alfredo and Richie, Tanner and Theriot, Casey and Kleiner, Manuel}, year={2023}, month={Dec} }
 @article{blakeley-ruiz_kleiner_2022, title={Considerations for constructing a protein sequence database for metaproteomics}, volume={20}, ISSN={["2001-0370"]}, url={http://dx.doi.org/10.1016/j.csbj.2022.01.018}, DOI={10.1016/j.csbj.2022.01.018}, abstractNote={Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies.}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, publisher={Elsevier BV}, author={Blakeley-Ruiz, J. Alfredo and Kleiner, Manuel}, year={2022}, pages={937–952} }
 @article{blakeley-ruiz_mcclintock_shrestha_poudel_yang_giannone_choo_podar_baghdoyan_lydic_et al._2022, title={Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice}, volume={2}, url={http://dx.doi.org/10.1038/s43705-022-00131-6}, DOI={10.1038/s43705-022-00131-6}, abstractNote={Abstract}, number={1}, journal={ISME Communications}, publisher={Springer Science and Business Media LLC}, author={Blakeley-Ruiz, J. Alfredo and McClintock, Carlee S. and Shrestha, Him K. and Poudel, Suresh and Yang, Zamin K. and Giannone, Richard J. and Choo, James J. and Podar, Mircea and Baghdoyan, Helen A. and Lydic, Ralph and et al.}, year={2022}, month={Aug} }
 @phdthesis{blakeley-ruiz_2020, title={Extracting detailed metabolic information and connections from mammalian gut microbiomes via metaproteomics}, url={https://trace.tennessee.edu/utk_graddiss/6194}, journal={University of Tennessee}, school={University of Tennessee}, author={Blakeley-Ruiz, Jose A.}, year={2020}, month={Dec} }
 @article{combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research_2019, url={http://dx.doi.org/10.1017/s0140525x18002911}, DOI={10.1017/s0140525x18002911}, abstractNote={Abstract}, journal={Behavioral and Brain Sciences}, year={2019} }
 @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_2019, url={http://dx.doi.org/10.1186/s40168-019-0631-8}, DOI={10.1186/s40168-019-0631-8}, abstractNote={The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn's disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn's disease patients' post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition.The measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products.The human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome's metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.}, journal={Microbiome}, year={2019}, month={Dec} }