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Shinn LM, Mansharamani A, Baer DJ, Novotny JA, Charron CS, Khan NA, Zhu R, Holscher HD. Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials. J Nutr 2024; 154:271-283. [PMID: 37949114 DOI: 10.1016/j.tjnut.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/11/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus revealing the potential of using metagenomic data for developing objective biomarkers of food intake. OBJECTIVES As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine-learning approach to identify fecal KEGG (Kyoto encyclopedia of genes and genomes) Orthology (KO) categories as biomarkers that accurately classify food intake. METHODS Data were aggregated from 5 controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. Deoxyribonucleic acid from preintervention and postintervention fecal samples underwent shotgun genomic sequencing. After preprocessing, sequences were aligned and functionally annotated with Double Index AlignMent Of Next-generation sequencing Data v2.0.11.149 and MEtaGenome ANalyzer v6.12.2, respectively. After the count normalization, the log of the fold change ratio for resulting KOs between pre- and postintervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine-learning models examining potential biomarkers in both single-food and multi-food models. RESULTS We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups using a random forest model to classify food intake into each food group's respective treatment and control arms, respectively. The mixed-food random forest achieved 81% accuracy. CONCLUSIONS Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.
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Affiliation(s)
- Leila M Shinn
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Aditya Mansharamani
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David J Baer
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Janet A Novotny
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Craig S Charron
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Naiman A Khan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States; Department of Kinesiology and Community Health, University of Illinois, Urbana, IL, United States
| | - Ruoqing Zhu
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, United States; National Center for Supercomputing Applications, University of Illinois, Urbana, IL, United States.
| | - Hannah D Holscher
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States; Department of Kinesiology and Community Health, University of Illinois, Urbana, IL, United States; National Center for Supercomputing Applications, University of Illinois, Urbana, IL, United States; Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, United States.
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Specific cyclic ADP-ribose phosphohydrolase obtained by mutagenic engineering of Mn 2+-dependent ADP-ribose/CDP-alcohol diphosphatase. Sci Rep 2018; 8:1036. [PMID: 29348648 PMCID: PMC5773619 DOI: 10.1038/s41598-017-18393-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/12/2017] [Indexed: 01/16/2023] Open
Abstract
Cyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. However, ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates. Recently, we showed that mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity: the best substrate of the mutant F37A + L196F + C253A is cADPR by a short difference, Cys253 mutation being essential for cADPR preference. Its proximity to the 'northern' ribose of cADPR in docking models indicates Cys253 is a steric constraint for cADPR positioning. Aiming to obtain a specific cADPR phosphohydrolase, new mutations were tested at Asp250, Val252, Cys253 and Thr279, all near the 'northern' ribose. First, the mutant F37A + L196F + C253G, with a smaller residue 253 (Ala > Gly), showed increased cADPR specificity. Then, the mutant F37A + L196F + V252A + C253G, with another residue made smaller (Val > Ala), displayed the desired specificity, with cADPR kcat/KM ≈20-200-fold larger than for any other substrate. When tested in nucleotide mixtures, cADPR was exhausted while others remained unaltered. We suggest that the specific cADPR phosphohydrolase, by cell or organism transgenesis, or the designed mutations, by genome editing, provide opportunities to study the effect of cADPR depletion on the many systems where it intervenes.
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