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Dr. Elizabeth Ryan
Department of Environmental and Radiological Health Science, Colorado State University, Fort Collin, CO USA

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0 Environmental Health
0 Microbiome and Gut Health
0 Nutrition and Cancer
0 Toxicology and Immunology
0 Food chemistry, metabolomics

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Accepted manuscript
Published: 21 July 2021 in Current Developments in Nutrition
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Environmental enteric dysfunction (EED) is associated with chronic gut inflammation affecting nutrient absorption and development of children, primarily in low- and middle-income countries. Several studies have shown that rice bran (RB) supplementation provides nutrients and modulates gut inflammation that may reduce risk for undernutrition. To evaluate daily RB dietary supplementation for six months on serum biomarkers in weaning infants and associated changes in serum and stool metabolites. A 6-month, randomized-controlled dietary intervention was conducted in a cohort of weaning 6-month-old infants in León, Nicaragua. Anthropometric indices were obtained at 6, 8, and 12 months. Serum and stool ionomics and metabolomics were completed at the end of the six-month intervention using Inductively coupled plasma mass spectrometry and Ultra-performance liquid chromatography tandem mass spectroscopy. The Alpha-1-acid glycoprotein, C-reactive protein and Glucagon-like peptide-2 serum EED biomarkers were measured by Enzyme-Linked Immunosorbant Assay ELISA. Twenty-four infants in the control group and 23 in the RB group successfully completed the 6-month dietary intervention with 90% dietary compliance. RB participants had higher concentrations of GLP-2 as compared to control participants at 12 months (median, (IQR): 743.53 (380.54) pg/ml vs. 592.50 (223.59) pg/ml; P = 0.04). Metabolite profiles showed significant fold differences of 39 serum metabolites and 44 stool metabolites from infants consuming RB compared to control, and with significant metabolic pathway enrichment scores of 4.7 for the tryptophan metabolic pathway, 5.7 for polyamine metabolism and 5.7 for fatty acid/acylcholine metabolic pathway in the RB group. No differences were detected in serum and stool trace elements or heavy metals following daily RB intake for six months. RB consumption influences a suite of metabolites associated with growth promotion and development, while also supporting nutrient absorption as measured by changes in serum glucagon-like peptide-2 in Nicaraguan infants. This clinical trial was registered at: https://clinicaltrials.gov (NCT02615886). Rice bran modulates glucagon-like peptide-2, serum and stool metabolites in weaning Nicaraguan infants. Clinical Trial Registry: NCT02615886 https://clinicaltrials.gov/ct2/show/NCT02615886

ACS Style

Luis E Zambrana; Annika M Weber; Erica C Borresen; Iman Zarei; Johann Perez; Claudia Perez; Iker Rodríguez; Sylvia Becker-Dreps; Lijuan Yuan; Samuel Vilchez; Elizabeth P Ryan. Daily Rice Bran Consumption for Six Months Influences Serum Glucagon-Like Peptide-2 And Metabolite Profiles Without Differences in Trace Elements and Heavy Metals in Weaning Nicaraguan Infants At 12 Months of Age. Current Developments in Nutrition 2021, 1 .

AMA Style

Luis E Zambrana, Annika M Weber, Erica C Borresen, Iman Zarei, Johann Perez, Claudia Perez, Iker Rodríguez, Sylvia Becker-Dreps, Lijuan Yuan, Samuel Vilchez, Elizabeth P Ryan. Daily Rice Bran Consumption for Six Months Influences Serum Glucagon-Like Peptide-2 And Metabolite Profiles Without Differences in Trace Elements and Heavy Metals in Weaning Nicaraguan Infants At 12 Months of Age. Current Developments in Nutrition. 2021; ():1.

Chicago/Turabian Style

Luis E Zambrana; Annika M Weber; Erica C Borresen; Iman Zarei; Johann Perez; Claudia Perez; Iker Rodríguez; Sylvia Becker-Dreps; Lijuan Yuan; Samuel Vilchez; Elizabeth P Ryan. 2021. "Daily Rice Bran Consumption for Six Months Influences Serum Glucagon-Like Peptide-2 And Metabolite Profiles Without Differences in Trace Elements and Heavy Metals in Weaning Nicaraguan Infants At 12 Months of Age." Current Developments in Nutrition , no. : 1.

Journal article
Published: 13 July 2021 in BMC Infectious Diseases
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Background SARS-CoV-2 has swept across the globe, causing millions of deaths worldwide. Though most survive, many experience symptoms of COVID-19 for months after acute infection. Successful prevention and treatment of acute COVID-19 infection and its associated sequelae is dependent on in-depth knowledge of viral pathology across the spectrum of patient phenotypes and physiologic responses. Longitudinal biobanking provides a valuable resource of clinically integrated, easily accessed, and quality-controlled samples for researchers to study differential multi-organ system responses to SARS-CoV-2 infection, post-acute sequelae of COVID-19 (PASC), and vaccination. Methods Adults with a history of a positive SARS-CoV-2 nasopharyngeal PCR are actively recruited from the community or hospital settings to enroll in the Northern Colorado SARS-CoV-2 Biorepository (NoCo-COBIO). Blood, saliva, stool, nasopharyngeal specimens, and extensive clinical and demographic data are collected at 4 time points over 6 months. Patients are assessed for PASC during longitudinal follow-up by physician led symptom questionnaires and physical exams. This clinical trial registration is NCT04603677. Results We have enrolled and collected samples from 119 adults since July 2020, with 66% follow-up rate. Forty-nine percent of participants assessed with a symptom surveillance questionnaire (N = 37 of 75) had PASC at any time during follow-up (up to 8 months post infection). Ninety-three percent of hospitalized participants developed PASC, while 23% of those not requiring hospitalization developed PASC. At 90–174 days post SARS-CoV-2 diagnosis, 67% of all participants had persistent symptoms (N = 37 of 55), and 85% percent of participants who required hospitalization during initial infection (N = 20) still had symptoms. The most common symptoms reported after 15 days of infection were fatigue, loss of smell, loss of taste, exercise intolerance, and cognitive dysfunction. Conclusions Patients who were hospitalized for COVID-19 were significantly more likely to have PASC than those not requiring hospitalization, however 23% of patients who were not hospitalized also developed PASC. This patient-matched, multi-matrix, longitudinal biorepository from COVID-19 survivors with and without PASC will allow for current and future research to better understand the pathophysiology of disease and to identify targeted interventions to reduce risk for PASC. Registered 27 October 2020 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04603677.

ACS Style

Stephanie M. LaVergne; Sophia Stromberg; Bridget A. Baxter; Tracy L. Webb; Taru S. Dutt; Kailey Berry; Madison Tipton; Jared Haberman; Benjamin R. Massey; Kim McFann; Omar Alnachoukati; Linda Zier; Thomas Heacock; Gregory D. Ebel; Marcela Henao-Tamayo; Julie Dunn; Elizabeth P. Ryan. A longitudinal SARS-CoV-2 biorepository for COVID-19 survivors with and without post-acute sequelae. BMC Infectious Diseases 2021, 21, 1 -9.

AMA Style

Stephanie M. LaVergne, Sophia Stromberg, Bridget A. Baxter, Tracy L. Webb, Taru S. Dutt, Kailey Berry, Madison Tipton, Jared Haberman, Benjamin R. Massey, Kim McFann, Omar Alnachoukati, Linda Zier, Thomas Heacock, Gregory D. Ebel, Marcela Henao-Tamayo, Julie Dunn, Elizabeth P. Ryan. A longitudinal SARS-CoV-2 biorepository for COVID-19 survivors with and without post-acute sequelae. BMC Infectious Diseases. 2021; 21 (1):1-9.

Chicago/Turabian Style

Stephanie M. LaVergne; Sophia Stromberg; Bridget A. Baxter; Tracy L. Webb; Taru S. Dutt; Kailey Berry; Madison Tipton; Jared Haberman; Benjamin R. Massey; Kim McFann; Omar Alnachoukati; Linda Zier; Thomas Heacock; Gregory D. Ebel; Marcela Henao-Tamayo; Julie Dunn; Elizabeth P. Ryan. 2021. "A longitudinal SARS-CoV-2 biorepository for COVID-19 survivors with and without post-acute sequelae." BMC Infectious Diseases 21, no. 1: 1-9.

Preprint content
Published: 07 May 2021
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BackgroundSARS-CoV-2 has swept across the globe, causing millions of deaths worldwide. Though most survive, many experience symptoms of COVID-19 for months after acute infection. Successful prevention and treatment of acute COVID-19 infection and its associated sequelae is dependent on in-depth knowledge of viral pathology across the spectrum of patient phenotypes and physiologic responses. Longitudinal biobanking provides a valuable resource of clinically integrated, easily accessed, and quality-controlled samples for researchers to study differential multi-organ system responses to SARS-CoV-2 infection, post-acute sequelae of COVID-19 (PASC), and vaccination. MethodsAdults with a history of a positive SARS-CoV-2 nasopharyngeal PCR are actively recruited from the community or hospital settings to enroll in the Northern Colorado SARS-CoV-2 Biorepository (NoCo-COBIO). Blood, saliva, stool, nasopharyngeal specimens, and extensive clinical and demographic data are collected at 4 time points over 6 months. Patients are assessed for PASC during longitudinal follow-up by physician led symptom questionnaires and physical exams. This clinical trial registration is NCT05603677.ResultsWe have enrolled and collected samples from 119 adults since July 2020, with 66% follow-up rate. Forty-nine percent of participants assessed with a symptom surveillance questionnaire (N=37 of 75) had PASC at any time during follow-up (up to 8 months post infection). Ninety-three percent of hospitalized participants developed PASC, while 23% of those not requiring hospitalization developed PASC. At 90-174 days post SARS-CoV-2 diagnosis, 67% of all participants had persistent symptoms (N=37 of 55), and 85% percent of participants who required hospitalization during initial infection (N=20) still had symptoms. The most common symptoms reported after 15 days of infection were fatigue, loss of smell, loss of taste, exercise intolerance, and cognitive dysfunction. ConclusionsPatients who were hospitalized for COVID-19 were significantly more likely to have PASC than those not requiring hospitalization, however 23% of patients who were not hospitalized also developed PASC. This patient-matched, multi-matrix, longitudinal biorepository from COVID-19 survivors with and without PASC will allow for current and future research to better understand the pathophysiology of disease and to identify targeted interventions to reduce risk for PASC. Registered 27 October 2020 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04603677.

ACS Style

Stephanie M LaVergne; Stromberg Sophia; Bridget A Baxter; Tracy L Webb; Taru S Dutt; Kailey Berry; Madison Tipton; Jared Haberman; Benjamin R Massey; Kim McFann; Omar Alnachoukati; Linda Zier; Thomas Heacock; Greg Ebel; Marcela Henao-Tamayo; Julie Dunn; Elizabeth P Ryan. A Longitudinal SARS-CoV-2 Biorepository for COVID-19 Survivors with and without Post-Acute Sequelae. 2021, 1 .

AMA Style

Stephanie M LaVergne, Stromberg Sophia, Bridget A Baxter, Tracy L Webb, Taru S Dutt, Kailey Berry, Madison Tipton, Jared Haberman, Benjamin R Massey, Kim McFann, Omar Alnachoukati, Linda Zier, Thomas Heacock, Greg Ebel, Marcela Henao-Tamayo, Julie Dunn, Elizabeth P Ryan. A Longitudinal SARS-CoV-2 Biorepository for COVID-19 Survivors with and without Post-Acute Sequelae. . 2021; ():1.

Chicago/Turabian Style

Stephanie M LaVergne; Stromberg Sophia; Bridget A Baxter; Tracy L Webb; Taru S Dutt; Kailey Berry; Madison Tipton; Jared Haberman; Benjamin R Massey; Kim McFann; Omar Alnachoukati; Linda Zier; Thomas Heacock; Greg Ebel; Marcela Henao-Tamayo; Julie Dunn; Elizabeth P Ryan. 2021. "A Longitudinal SARS-CoV-2 Biorepository for COVID-19 Survivors with and without Post-Acute Sequelae." , no. : 1.

Journal article
Published: 15 February 2021 in Metabolites
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Rice bran (RB) corresponds to the outer layers of whole grain rice and contains several phenolic compounds (PCs) that make it an interesting functional food ingredient. PC richness is enhanced in pigmented RB varieties and requires effective ways of extraction of these compounds. Therefore, we investigated conventional and deep eutectic solvents (DES) extraction methods to recover a wide array of PCs from red and black RB. The RB were extracted with ethanol/water (60:40, v/v) and two DES (choline chloride/1.2-propanediol/water, 1:1:1 and choline chloride/lactic acid, 1:10, mole ratios), based on Generally Recognized as Safe (GRAS) components. Besides the quantification of the most typical phenolic acids of cereals, nontargeted metabolomic approaches were applied to PCs profiling in the extracts. Globally, metabolomics revealed 89 PCs belonging to flavonoids (52%), phenolic acids (33%), other polyphenols (8%), lignans (6%) and stilbenes (1%) classes. All extracts, whatever the solvents, were highly concentrated in the main phenolic acids found in cereals (37–66 mg/100 g in black RB extracts vs. 6–20 mg/100 g in red RB extracts). However, the PC profile was highly dependent on the extraction solvent and specific PCs were extracted using the acidic DES. The PC-enriched DES extracts demonstrated interesting DPPH scavenging activity, which makes them candidates for novel antioxidant formulations.

ACS Style

Millena Santos; Nathalie Barouh; Erwann Durand; Bruno Baréa; Mélina Robert; Valérie Micard; Valérie Lullien-Pellerin; Pierre Villeneuve; Luiz Cameron; Elizabeth Ryan; Mariana Ferreira; Claire Bourlieu-Lacanal. Metabolomics of Pigmented Rice Coproducts Applying Conventional or Deep Eutectic Extraction Solvents Reveal a Potential Antioxidant Source for Human Nutrition. Metabolites 2021, 11, 110 .

AMA Style

Millena Santos, Nathalie Barouh, Erwann Durand, Bruno Baréa, Mélina Robert, Valérie Micard, Valérie Lullien-Pellerin, Pierre Villeneuve, Luiz Cameron, Elizabeth Ryan, Mariana Ferreira, Claire Bourlieu-Lacanal. Metabolomics of Pigmented Rice Coproducts Applying Conventional or Deep Eutectic Extraction Solvents Reveal a Potential Antioxidant Source for Human Nutrition. Metabolites. 2021; 11 (2):110.

Chicago/Turabian Style

Millena Santos; Nathalie Barouh; Erwann Durand; Bruno Baréa; Mélina Robert; Valérie Micard; Valérie Lullien-Pellerin; Pierre Villeneuve; Luiz Cameron; Elizabeth Ryan; Mariana Ferreira; Claire Bourlieu-Lacanal. 2021. "Metabolomics of Pigmented Rice Coproducts Applying Conventional or Deep Eutectic Extraction Solvents Reveal a Potential Antioxidant Source for Human Nutrition." Metabolites 11, no. 2: 110.

Journal article
Published: 03 February 2021 in Biomedicines
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Rice bran, removed from whole grain rice for white rice milling, has demonstrated efficacy for the control and suppression of colitis and colon cancer in multiple animal models. Dietary rice bran intake was shown to modify human stool metabolites as a result of modifications to metabolism by gut microbiota. In this study, human stool microbiota from colorectal cancer (CRC) survivors that consumed rice bran daily was examined by fecal microbiota transplantation (FMT) for protection from azoxymethane and dextran sodium sulfate (AOM/DSS) induced colon carcinogenesis in germ-free mice. Mice transfaunated with rice bran-modified microbiota communities (RMC) harbored fewer neoplastic lesions in the colon and displayed distinct enrichment of Flavonifractor and Oscillibacter associated with colon health, and the depletion of Parabacteroides distasonis correlated with increased tumor burden. Two anti-cancer metabolites, myristoylcarnitine and palmitoylcarnitine were increased in the colon of RMC transplanted mice. Trimethylamine-N-oxide (TMAO) and tartarate that are implicated in CRC development were reduced in murine colon tissue after FMT with rice bran-modified human microbiota. Findings from this study show that rice bran modified gut microbiota from humans confers protection from colon carcinogenesis in mice and suggests integrated dietary-FMT intervention strategies should be tested for colorectal cancer control, treatment, and prevention.

ACS Style

Kristopher Parker; Akhilendra Maurya; Hend Ibrahim; Sangeeta Rao; Petronella Hove; Dileep Kumar; Rama Kant; Bupinder Raina; Rajesh Agarwal; Kristine Kuhn; Komal Raina; Elizabeth Ryan. Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation. Biomedicines 2021, 9, 144 .

AMA Style

Kristopher Parker, Akhilendra Maurya, Hend Ibrahim, Sangeeta Rao, Petronella Hove, Dileep Kumar, Rama Kant, Bupinder Raina, Rajesh Agarwal, Kristine Kuhn, Komal Raina, Elizabeth Ryan. Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation. Biomedicines. 2021; 9 (2):144.

Chicago/Turabian Style

Kristopher Parker; Akhilendra Maurya; Hend Ibrahim; Sangeeta Rao; Petronella Hove; Dileep Kumar; Rama Kant; Bupinder Raina; Rajesh Agarwal; Kristine Kuhn; Komal Raina; Elizabeth Ryan. 2021. "Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation." Biomedicines 9, no. 2: 144.

Journal article
Published: 24 December 2020 in Cancer Prevention Research
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Navy beans contain bioactive phytochemicals with colon cancer prevention properties as demonstrated in carcinogen-induced animal models. Human studies support that dietary navy bean intake modulates metabolism by the gut microbiome. This study investigated the effect of navy bean ingestion on plasma and urine metabolite profiles of overweight and obese colorectal cancer (CRC) survivors. Twenty participants completed a single-blinded, randomized-controlled dietary intervention with pre-cooked navy beans (35g bean powder/day) or control (0g/day) for 4 weeks. Plasma and urine were collected at baseline, 2 weeks and 4 weeks following consumption. Non-targeted metabolomics was applied to study meals and snacks, navy beans, plasma, and urine. Increased navy bean consumption was hypothesized to a) delineate dietary biomarkers and b) promote metabolic shifts relevant for cancer protection in the plasma and urine metabolome. At 4 weeks, 16 plasma and 16 urine metabolites were significantly different in the navy bean intervention group compared to placebo-control (p< 0.05). Increased plasma 2,3-dihydroxy-2-methylbutyrate (1.34-fold), S-methylcysteine (1.92-fold), and pipecolate (3.89-fold), and urine S-adenosylhomocysteine (2.09-fold) and cysteine (1.60-fold) represent metabolites with cancer protective actions following navy bean consumption. Diet-derived metabolites were detected in plasma or urine and confirmed for presence in the navy bean intervention meals and snacks. These included 3-(4-hydroxyphenyl)propionate, betaine, pipecolate, S-methylcysteine, choline, eicosapentaenoate (20:5n3), benzoate, S-adenosylhomocysteine, N-delta-acetylornithine, cysteine, 3-(4-hydroxyphenyl)lactate, gentisate, hippurate, 4-hydroxyhippurate, and salicylate. The navy bean dietary intervention for 4 weeks showed changes to pathways of metabolic importance to CRC prevention and merit continued attention for dietary modulation in future high-risk cohort investigations.

ACS Style

Iman Zarei; Bridget A Baxter; Renee C Oppel; Erica C Borresen; Regina J. Brown; Elizabeth P Ryan. Plasma and Urine Metabolite Profiles Impacted by Increased Dietary Navy Bean Intake in Colorectal Cancer Survivors: a randomized-controlled trial. Cancer Prevention Research 2020, 1 .

AMA Style

Iman Zarei, Bridget A Baxter, Renee C Oppel, Erica C Borresen, Regina J. Brown, Elizabeth P Ryan. Plasma and Urine Metabolite Profiles Impacted by Increased Dietary Navy Bean Intake in Colorectal Cancer Survivors: a randomized-controlled trial. Cancer Prevention Research. 2020; ():1.

Chicago/Turabian Style

Iman Zarei; Bridget A Baxter; Renee C Oppel; Erica C Borresen; Regina J. Brown; Elizabeth P Ryan. 2020. "Plasma and Urine Metabolite Profiles Impacted by Increased Dietary Navy Bean Intake in Colorectal Cancer Survivors: a randomized-controlled trial." Cancer Prevention Research , no. : 1.

Preprint content
Published: 23 December 2020
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Probiotics merit testing as alternatives to conventional antibiotics and are receiving increased attention for efficacy against multi-drug resistant pathogen infections. This study hypothesis was that the Gram-positive probiotic,L. rhamnosusGG (LGG) and Gram-negativeE. coliNissle (ECN) secrete distinct proteins and metabolites to suppress pathogen growth. LGG and ECN cell free supernatants were tested in a dose-dependent manner for differential growth suppression ofSalmonellaTyphimurium,Escherichia coli, andKlebsiella oxytocathat harbor antimicrobial resistance (AMR). Across supernatant doses, LGG was 6.27% to 20.55% more effective than ECN at suppressing AMR pathogen growth. Proteomics and metabolomics were performed to identify pathways that distinguished LGG and ECN for antimicrobial functions. From the 667 detected metabolites in probiotic cell free supernatants, 304 metabolites had significantly different relative abundance between LGG and ECN, and only 5 and 6 unique metabolites were identified for LGG and ECN respectively. LGG and ECN differences involved amino acid, energy and nucleotide metabolism. Proteomics analysis of ECN and LGG cell free supernatants identified distinctions in 87 proteins, where many were related to carbohydrate and energy metabolism. Integration of genome-proteome-metabolome signatures from LGG and ECN with predictive metabolic modeling supported differential use of substrates by these two probiotics as drivers of antimicrobial actions. ECN metabolized a range of carbon sources, largely purines, whereas LGG consumed primarily carbohydrates. Understanding functional biosynthesis, utilization and secretion of bioactive metabolites and proteins from genetically distinct probiotics will guide strategic approaches for developing antibiotic alternatives and for controlling spread of multi-drug resistant pathogens. Importance Probiotics are practical alternatives for protection against antimicrobial resistant pathogens. Bioactive probiotics molecules merit further investigation using high throughput - omic approaches. This study identified functional differences between Gram-positiveL. rhamnosusGG (LGG) and Gram-negativeE. coliNissle (ECN) probiotics that suppressed the growth of antimicrobial resistantS.Typhimurium,K. oxytoca, andE. coli. Proteomes and metabolomes of the probiotic cell free supernatants showed metabolic differences between LGG and ECN for mediating pathogen growth suppression. Metabolites distinguishing LGG versus ECN growth suppression included carbohydrates, lipids, amino acids, and nucleic acids. The metabolic flux differences between ECN and LGG, which coincided with observed separations in the proteomes and metabolomes, was hypothesized to explain the differential suppression of AMR pathogens. Integrated metabolite and protein signatures produced by each probiotic merit attention as adjuvant therapeutics for antimicrobial resistant infections.

ACS Style

Petronella R. Hove; Nora Jean Nealon; Siu Hung Joshua Chan; Shea M. Boyer; Hannah B. Haberecht; Elizabeth P. Ryan. Metabolomics and proteomics ofL. rhamnosusGG andE. coliNissle probiotic supernatants identify distinct pathways that mediate growth suppression of antimicrobial-resistant pathogens. 2020, 1 .

AMA Style

Petronella R. Hove, Nora Jean Nealon, Siu Hung Joshua Chan, Shea M. Boyer, Hannah B. Haberecht, Elizabeth P. Ryan. Metabolomics and proteomics ofL. rhamnosusGG andE. coliNissle probiotic supernatants identify distinct pathways that mediate growth suppression of antimicrobial-resistant pathogens. . 2020; ():1.

Chicago/Turabian Style

Petronella R. Hove; Nora Jean Nealon; Siu Hung Joshua Chan; Shea M. Boyer; Hannah B. Haberecht; Elizabeth P. Ryan. 2020. "Metabolomics and proteomics ofL. rhamnosusGG andE. coliNissle probiotic supernatants identify distinct pathways that mediate growth suppression of antimicrobial-resistant pathogens." , no. : 1.

Preprint content
Published: 14 February 2020
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Diet is one of the prominent determinants of gut microbiota composition significantly impacting human health. Recent studies with dietary supplements such as rice bran and quercetin have been shown to provide a beneficial impact on the host by positively influencing the gut microbiota. However, the specific bacterial species impacted when rice bran or quercetin is present in the diet is not well understood. Therefore, in this study, we used a minibioreactor array system as a model to determine the effect of quercetin and rice bran individually, as well as in combination, on gut microbiota without the confounding host factors. We found that rice bran exerts higher shift in gut microbiome composition when compared to quercetin. At the species level, Acidaminococcus intestini was the only significantly enriched taxa when quercetin was supplemented, while 15 species were enriched in rice bran supplementation and 13 were enriched when quercetin and rice bran were supplemented in combination. When comparing the short chain fatty acid production, quercetin supplementation significantly enriched isobutyrate production while propionate dominated the quercetin and rice bran combined group. Higher levels of propionate were highly correlated to the lower abundance of the potentially pathogenic Enterobacteriaceae family. These findings suggest that the combination of rice bran and quercetin serve to enrich beneficial bacteria and reduce potential opportunistic pathogens. However, further in vivo studies are necessary to determine the synergistic effect of rice bran and quercetin on host health and immunity.ImportanceRice bran and quercetin are dietary components that shape host health by interacting with the gut microbiome. Both these substrates have been reported to provide nutritional and immunological benefits individually. However, considering the complexity of the human diet, it is useful to determine how the combination of food ingredients such as rice bran and quercetin influences the human gut microbiota. Our study provides insights into how these ingredients influence microbiome composition alone and in combination in vitro. This will allow us to identify which species in the gut microbiome are responsible for biotransformation of these dietary ingredients.. Such information is helpful for the development of synbiotics to improve gut health and immunity.

ACS Style

Sudeep Ghimire; Supapit Wongkuna; Ranjini Sankaranarayanan; Elizabeth P. Ryan; G. Jayarama Bhat; Joy Scaria. Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model. 2020, 1 .

AMA Style

Sudeep Ghimire, Supapit Wongkuna, Ranjini Sankaranarayanan, Elizabeth P. Ryan, G. Jayarama Bhat, Joy Scaria. Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model. . 2020; ():1.

Chicago/Turabian Style

Sudeep Ghimire; Supapit Wongkuna; Ranjini Sankaranarayanan; Elizabeth P. Ryan; G. Jayarama Bhat; Joy Scaria. 2020. "Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model." , no. : 1.

Journal article
Published: 21 January 2020 in World Journal of Gastroenterology
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Obesity is a risk factor for colorectal cancer, yet metabolic distinctions between healthy right and left colon tissue, before cancer is diagnosed, remains largely unknown. This study compared right-ascending and left-descending colon tissue metabolomes to identify differences from the stool metabolome in normal weight, overweight, and obese adults. To examine right and left colon tissue metabolites according to body mass index that may serve as mechanistic targets for interventions and biomarkers for colon cancer risk. Global, non-targeted metabolomics was applied to assess right-ascending and left-descending colon tissue collected from healthy adults undergoing screening colonoscopies to test the hypothesis that BMI differentially impacts colon tissue metabolite profiles. The colon tissue and stool metabolome of healthy adults (n = 24) was analyzed for metabolite signatures and metabolic pathway networks implicated in progression of colorectal cancer. Ascending and descending colon contained 504 host, food, and microbiota-derived metabolites from normal weight, overweight and obese adults grouped according to body mass index. Amino acids, lipids, and nucleotides were among the chemical types that further differentiated from the stool metabolite profiles. Normal weight adults had 46 significantly different metabolites between ascending and descending colon tissue locations, whereas there were 37 metabolite differences in overweight and 28 metabolite differences for obese adults (P < 0.05). Obese adults had trimethylamine N-oxide, endocannabinoids and monoacylglycerols with different relative abundances identified between ascending and descending colon. Primary and secondary bile acids, vitamins, and fatty acids also showed marked relative abundance differences in colon tissue from overweight/obese adults. There were metabolite profile differences between right-ascending and left-descending colon tissue in healthy adults. Colon lipids and other metabolites in obese and overweight adults were distinguished from normal weight participants and associated with gut inflammation, nutrient absorption, and products of microbiota metabolism.

ACS Style

Bridget A Baxter; Kristopher D Parker; Michael J Nosler; Sangeeta Rao; Rebecca Craig; Catherine Seiler; Elizabeth P Ryan. Metabolite profile comparisons between ascending and descending colon tissue in healthy adults. World Journal of Gastroenterology 2020, 26, 335 -352.

AMA Style

Bridget A Baxter, Kristopher D Parker, Michael J Nosler, Sangeeta Rao, Rebecca Craig, Catherine Seiler, Elizabeth P Ryan. Metabolite profile comparisons between ascending and descending colon tissue in healthy adults. World Journal of Gastroenterology. 2020; 26 (3):335-352.

Chicago/Turabian Style

Bridget A Baxter; Kristopher D Parker; Michael J Nosler; Sangeeta Rao; Rebecca Craig; Catherine Seiler; Elizabeth P Ryan. 2020. "Metabolite profile comparisons between ascending and descending colon tissue in healthy adults." World Journal of Gastroenterology 26, no. 3: 335-352.

Journal article
Published: 09 December 2019 in Beneficial Microbes
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This study investigated gut microbiota composition along with food, host, and microbial derived metabolites in the colon and systemic circulation of healthy mice following dietary rice bran and fermented rice bran intake. Adult male BALB/c mice were fed a control diet or one of two experimental diets containing 10% w/w rice bran fermented by Bifidobacterium longum or 10% w/w non-fermented rice bran for 15 weeks. Metabolomics was performed on the study diets (food), the murine colon and whole blood. These were analysed in concert with 16S rRNA amplicon sequencing of faeces, caecum, and colon microbiomes. Principal components analysis of murine microbiota composition displayed marked separation between control and experimental diets, and between faecal and tissue (caecum and colon) microbiomes. Colon and caecal microbiomes in both experimental diet groups showed enrichment of Roseburia, Lachnospiraceae, and Clostridiales related amplicon sequence variants compared to control. Bacterial composition was largely similar between experimental diets. Metabolite profiling revealed 530 small molecules comprising of 39% amino acids and 21% lipids that had differential abundances across food, colon, and blood matrices, and statistically significant between the control, rice bran, and fermented rice bran groups. The amino acid metabolite, N-delta-acetylornithine, was notably increased by B. longum rice bran fermentation when compared to non-fermented rice bran in food, colon, and blood. These findings support that dietary intake of rice bran fermented with B. longum modulates multiple metabolic pathways important to the gut and overall health.

ACS Style

N.J. Nealon; K.D. Parker; P. Lahaie; H. Ibrahim; A.K. Maurya; K. Raina; E.P. Ryan. Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome. Beneficial Microbes 2019, 10, 823 -839.

AMA Style

N.J. Nealon, K.D. Parker, P. Lahaie, H. Ibrahim, A.K. Maurya, K. Raina, E.P. Ryan. Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome. Beneficial Microbes. 2019; 10 (8):823-839.

Chicago/Turabian Style

N.J. Nealon; K.D. Parker; P. Lahaie; H. Ibrahim; A.K. Maurya; K. Raina; E.P. Ryan. 2019. "Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome." Beneficial Microbes 10, no. 8: 823-839.

Chapter
Published: 01 December 2019 in Pets as Sentinels, Forecasters and Promoters of Human Health
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Companion animal exposures to pesticides were investigated to describe instances in which shared exposures may be useful to understand impacts on the health of humans. Several distinct types and classes of pesticides that have wide-ranging sources of exposure across animals, people, and environments are discussed in a “One Health” context. The ubiquity of pesticides in surface waters and drinking water may be an important source of persistent pesticide exposures to animals and people, and we can appreciate that low doses of chemical mixtures are the reality. While exposures may accumulate in any animal or human host over different lengths of time (i.e., days, months, years), not all mechanistic studies utilize relevant concentrations nor, can the levels be used to predict shared health risks. Pet animals already serve as a high sentinel value for humans in cancer research and other shared diseases. This chapter highlights common food and water sources from household and agricultural settings for selected pesticides and the potential impacts on animal and human health. The application of novel methodologies such as high-throughput chemical screening and predictive modeling, may be a future research opportunity to advance our understanding of pets as sentinels of exposure to chemical mixtures. Baseline data is needed if we intend to design interventions that will prevent or mitigate the negative, adverse effects of pesticide exposures throughout the lifespan and across generations of people and companion animals.

ACS Style

Basak Aslan; Lindsey Viola; Shivender Singh Saini; Jonathan Stockman; Elizabeth P. Ryan. Pets as Sentinels of Human Exposure to Pesticides and Co-exposure Concerns with Other Contaminants/Toxicants. Pets as Sentinels, Forecasters and Promoters of Human Health 2019, 47 -64.

AMA Style

Basak Aslan, Lindsey Viola, Shivender Singh Saini, Jonathan Stockman, Elizabeth P. Ryan. Pets as Sentinels of Human Exposure to Pesticides and Co-exposure Concerns with Other Contaminants/Toxicants. Pets as Sentinels, Forecasters and Promoters of Human Health. 2019; ():47-64.

Chicago/Turabian Style

Basak Aslan; Lindsey Viola; Shivender Singh Saini; Jonathan Stockman; Elizabeth P. Ryan. 2019. "Pets as Sentinels of Human Exposure to Pesticides and Co-exposure Concerns with Other Contaminants/Toxicants." Pets as Sentinels, Forecasters and Promoters of Human Health , no. : 47-64.

Journal article
Published: 26 September 2019 in Scientific Reports
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Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens and diarrhea, and warrants attention for improvement of environmental enteric dysfunction (EED) in children. EED is a subclinical condition associated with stunting due to impaired nutrient absorption. This study investigated the effects of rice bran supplementation on weight for age and length for age z-scores (WAZ, LAZ), EED stool biomarkers, as well as microbiota and metabolome signatures in weaning infants from 6 to 12 months old that reside in Nicaragua and Mali. Healthy infants were randomized to a control (no intervention) or a rice bran group that received daily supplementation with increasing doses at each month (1–5 g/day). Stool microbiota were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible to support changes in LAZ from 6–8 and 8–12 months of age in Nicaragua and Mali infants when compared to control. WAZ was significantly improved only for Mali infants at 8 and 12 months. Mali and Nicaraguan infants showed major differences in the overall gut microbiota and metabolome composition and structure at baseline, and thus each country cohort demonstrated distinct microbial and metabolite profile responses to rice bran supplementation when compared to control. Rice bran is a practical dietary intervention strategy that merits development in rice-growing regions that have a high prevalence of growth stunting due to malnutrition and diarrheal diseases. Rice is grown as a staple food, and the bran is used as animal feed or wasted in many low- and middle-income countries where EED and stunting is prevalent.

ACS Style

Luis E. Zambrana; Starin McKeen; Hend Ibrahim; Iman Zarei; Erica C. Borresen; Lassina Doumbia; Abdoulaye Boré; Alima Cissoko; Seydou Douyon; Karim Koné; Johann Perez; Claudia Perez; Ann Hess; Zaid Abdo; Lansana Sangaré; Ababacar Maiga; Sylvia Becker-Dreps; Lijuan Yuan; Ousmane Koita; Samuel Vilchez; Elizabeth P. Ryan. Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. Scientific Reports 2019, 9, 1 -18.

AMA Style

Luis E. Zambrana, Starin McKeen, Hend Ibrahim, Iman Zarei, Erica C. Borresen, Lassina Doumbia, Abdoulaye Boré, Alima Cissoko, Seydou Douyon, Karim Koné, Johann Perez, Claudia Perez, Ann Hess, Zaid Abdo, Lansana Sangaré, Ababacar Maiga, Sylvia Becker-Dreps, Lijuan Yuan, Ousmane Koita, Samuel Vilchez, Elizabeth P. Ryan. Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. Scientific Reports. 2019; 9 (1):1-18.

Chicago/Turabian Style

Luis E. Zambrana; Starin McKeen; Hend Ibrahim; Iman Zarei; Erica C. Borresen; Lassina Doumbia; Abdoulaye Boré; Alima Cissoko; Seydou Douyon; Karim Koné; Johann Perez; Claudia Perez; Ann Hess; Zaid Abdo; Lansana Sangaré; Ababacar Maiga; Sylvia Becker-Dreps; Lijuan Yuan; Ousmane Koita; Samuel Vilchez; Elizabeth P. Ryan. 2019. "Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali." Scientific Reports 9, no. 1: 1-18.

Review
Published: 04 April 2019 in Sustainability
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Cities are increasingly turning to food policy plans to support goals related to food access, food security, the environment, and economic development. This paper investigates ways that rural farmers, communities, and economies can both support and be supported by metropolitan food-focused initiatives. Specifically, our research question asked what opportunities and barriers exist to developing food policies that support urban food goals, particularly related to local procurement, as well as rural economic development. To address this question, we described and analyzed a meeting of urban stakeholders and larger-scale rural producers related to Colorado’s Denver Food Vision and Plan. We documented and explored “findings” gleaned from a supply chain diagraming and data compilation process that were then used to inform an event that brought together diverse supply chain partners. Three findings stand out. First, facilitating dialog between urban food policymakers and rural producers to understand potential tensions, mitigate such tensions, and capitalize on opportunities is essential. Second, perceptions and expectations surrounding “good food” are nuanced—a timely finding given the number of preferred procurement programs emerging across the county. Third, critical evaluation is needed across a diverse set of value chain strategies (e.g., conventional and alternative distribution) if food policy intends to support heterogeneous producers, their communities, and urban food policy goals.

ACS Style

Becca Jablonski; Michael Carolan; James Hale; Dawn Thilmany McFadden; Erin Love; Libby Christensen; Tabitha Covey; Laura Bellows; Rebecca Cleary; Olaf David; Kevin Jablonski; Andrew Jones; Paul Meiman; Jason Quinn; Elizabeth Ryan; Meagan Schipanski; Hailey Summers; Mark Uchanski. Connecting Urban Food Plans to the Countryside: Leveraging Denver’s Food Vision to Explore Meaningful Rural–Urban Linkages. Sustainability 2019, 11, 2022 .

AMA Style

Becca Jablonski, Michael Carolan, James Hale, Dawn Thilmany McFadden, Erin Love, Libby Christensen, Tabitha Covey, Laura Bellows, Rebecca Cleary, Olaf David, Kevin Jablonski, Andrew Jones, Paul Meiman, Jason Quinn, Elizabeth Ryan, Meagan Schipanski, Hailey Summers, Mark Uchanski. Connecting Urban Food Plans to the Countryside: Leveraging Denver’s Food Vision to Explore Meaningful Rural–Urban Linkages. Sustainability. 2019; 11 (7):2022.

Chicago/Turabian Style

Becca Jablonski; Michael Carolan; James Hale; Dawn Thilmany McFadden; Erin Love; Libby Christensen; Tabitha Covey; Laura Bellows; Rebecca Cleary; Olaf David; Kevin Jablonski; Andrew Jones; Paul Meiman; Jason Quinn; Elizabeth Ryan; Meagan Schipanski; Hailey Summers; Mark Uchanski. 2019. "Connecting Urban Food Plans to the Countryside: Leveraging Denver’s Food Vision to Explore Meaningful Rural–Urban Linkages." Sustainability 11, no. 7: 2022.

Research article
Published: 18 February 2019 in Journal of Environmental and Public Health
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WaterborneEscherichia coliare a major reservoir of antimicrobial resistance (AMR), including but not limited to extended-spectrum beta-lactamase (ESBL) andKlebsiella pneumoniaecarbapenemase (KPC) mechanisms. This study quantified and described ESBL- and KPC-producingE. coliin Northern Colorado from sewer water, surface water, and influent and effluent wastewater treatment sources. Total detected bacteria andE. coliabundances, and the percentages that contain ESBL and/or KPC, were compared between water sources. SeventyE. coliisolates from the various waters had drug resistance validated with a panel of 17 antibiotics using a broth microdilution assay. The diverse drug resistance observed acrossE. coliisolates was further documented by polymerase chain reaction of common ESBL genes and functional relatedness by PhenePlate assay-generated dendrograms ( n = 70 ). The totalE. coliabundance decreased through the water treatment process as expected, yet the percentages ofE. coliharboring ESBL resistance were increased (1.70%) in surface water. Whole-genome sequencing analysis was completed for 185 AMR genes in wastewaterE. coliisolates and confirmed the presence of diverse AMR gene classes (e.g., beta-lactams and efflux pumps) in isolate genomes. This study completed surveillance of AMR patterns inE. colithat reside in environmental water systems and suggests a role for integrating both phenotypic and genotypic profiling beyond ESBL and KPC mechanisms. AMR screening via multiple approaches may assist in the prevention of drug-resistantE. colispread from waters to animals and humans.

ACS Style

Hannah B. Haberecht; Nora Jean Nealon; Jake R. Gilliland; Amethyst V. Holder; Connor Runyan; Renee C. Oppel; Hend M. Ibrahim; Link Mueller; Forrest Schrupp; Samuel Vilchez; Linto Antony; Joy Scaria; Elizabeth P. Ryan. Antimicrobial-ResistantEscherichia colifrom Environmental Waters in Northern Colorado. Journal of Environmental and Public Health 2019, 2019, 1 -13.

AMA Style

Hannah B. Haberecht, Nora Jean Nealon, Jake R. Gilliland, Amethyst V. Holder, Connor Runyan, Renee C. Oppel, Hend M. Ibrahim, Link Mueller, Forrest Schrupp, Samuel Vilchez, Linto Antony, Joy Scaria, Elizabeth P. Ryan. Antimicrobial-ResistantEscherichia colifrom Environmental Waters in Northern Colorado. Journal of Environmental and Public Health. 2019; 2019 ():1-13.

Chicago/Turabian Style

Hannah B. Haberecht; Nora Jean Nealon; Jake R. Gilliland; Amethyst V. Holder; Connor Runyan; Renee C. Oppel; Hend M. Ibrahim; Link Mueller; Forrest Schrupp; Samuel Vilchez; Linto Antony; Joy Scaria; Elizabeth P. Ryan. 2019. "Antimicrobial-ResistantEscherichia colifrom Environmental Waters in Northern Colorado." Journal of Environmental and Public Health 2019, no. : 1-13.

Journal article
Published: 07 February 2019 in BMC Veterinary Research
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The first month of life possess significant challenges for dairy calves due to high susceptibility to digestive diseases. The objective of this study was to evaluate the effect of prebiotic supplementation with stabilized rice bran (SRB) in milk on health, immunity, and performance of pre-weaned organic dairy calves. Holstein heifer calves (n = 90) were enrolled at 6 ± 1 days old and monitored for 28 days, from July to August 2017. Calves were randomly assigned to a control (CTR; n = 45) or a treatment group (SRB; n = 45). The CTR group received milk alone and the SRB group received 120 g of SRB per day in milk to achieve a 10% w/w dose of the total calories. Daily health evaluations were conducted to score health status and disease severity (healthy, slightly affected, moderately or severely sick) of calves, through integrated assessment of diarrhea, dehydration, attitude, and milk intake. Body weights and fecal IgA quantification were completed on the first and last day of the study. Overall, weight gain and fecal IgA concentrations were not affected by the dietary addition of SRB. The total number of calf-days classified as healthy or sick were not different between treatment groups. Similarly, the number of calf-days categorized as slightly affected, moderately sick, or severely sick did not differ between treatment groups. Time to event analyses indicated a tendency for a treatment effect in the time to the first moderate case of diarrhea (P = 0.08), as well as in the time to recovery from diarrhea (P = 0.052), favoring control calves. These results indicated that the dietary addition of SRB in milk did not have an effect in health, immunity or performance of pre-weaned dairy calves.

ACS Style

Ana Velasquez-Munoz; Diego Manriquez; Sushil Paudyal; HyungChul Han; Robert Callan; Elizabeth P. Ryan; Pablo Pinedo. Effect of prebiotic supplementation with stabilized rice bran in milk of pre-weaned organic Holstein calves. BMC Veterinary Research 2019, 15, 1 -9.

AMA Style

Ana Velasquez-Munoz, Diego Manriquez, Sushil Paudyal, HyungChul Han, Robert Callan, Elizabeth P. Ryan, Pablo Pinedo. Effect of prebiotic supplementation with stabilized rice bran in milk of pre-weaned organic Holstein calves. BMC Veterinary Research. 2019; 15 (1):1-9.

Chicago/Turabian Style

Ana Velasquez-Munoz; Diego Manriquez; Sushil Paudyal; HyungChul Han; Robert Callan; Elizabeth P. Ryan; Pablo Pinedo. 2019. "Effect of prebiotic supplementation with stabilized rice bran in milk of pre-weaned organic Holstein calves." BMC Veterinary Research 15, no. 1: 1-9.

Preprint
Published: 26 January 2019
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Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens in mice and diarrhea in neonatal pigs, and warranted attention for improvement of environmental enteric dysfunction (EED) in children at risk. EED is a condition that drives childhood stunting via intestinal dysbiosis and impaired nutrient metabolism. This study investigated effects of rice bran supplementation on growth, EED biomarkers, gut microbiome and metabolome in weaning infants from 6 to 12 months old in Nicaragua and Mali. Healthy infants were randomized to a control group or rice bran group that received daily supplementation at increasing doses each month. Stool microbiomes were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible for infant growth, decreasing alpha-1 antitrypsin levels, and modulating gut microbiome and metabolome when compared to control. Rice bran merits investigation as a practical intervention strategy that could decrease EED prevalence and risk for children from low- and middle-income countries where rice is grown as a staple food, and bran is used as animal feed or wasted.One Sentence SummaryDietary rice bran supplementation during infant weaning from 6-12 months of age improved growth outcomes, modulated environmental enteric dysfunction biomarkers, and supported metabolism by the gut microbiome.The authors declare no competing financial or non financial interests to disclose as defined by Nature Research. There are also no other interests that might be perceived to influence the results and/or discussion reported in this paper.Correspondence and requests for materials should be addressed to Dr. Elizabeth Ryan ([email protected]).

ACS Style

Luis E. Zambrana; Starin A McKeen; Hend M Ibrahim; Iman Zarei; Erica C. Borresen; Lassina Doumbia; Abdoulaye Bore; Alima Cissoko; Seydou Douyon; Karim Kone; Johann Perez; Claudia Perez; Ann Hess; Zaid Abdo; Lansana Sangare; Ababacar Maiga; Sylvia Becker-Dreps; Lijuan Yuan; Ousmane Koita; Samuel Vilchez; Elizabeth P. Ryan; Hend Ibrahim. Rice bran supplementation modulates growth, microbiome and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. 2019, 530089 .

AMA Style

Luis E. Zambrana, Starin A McKeen, Hend M Ibrahim, Iman Zarei, Erica C. Borresen, Lassina Doumbia, Abdoulaye Bore, Alima Cissoko, Seydou Douyon, Karim Kone, Johann Perez, Claudia Perez, Ann Hess, Zaid Abdo, Lansana Sangare, Ababacar Maiga, Sylvia Becker-Dreps, Lijuan Yuan, Ousmane Koita, Samuel Vilchez, Elizabeth P. Ryan, Hend Ibrahim. Rice bran supplementation modulates growth, microbiome and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. . 2019; ():530089.

Chicago/Turabian Style

Luis E. Zambrana; Starin A McKeen; Hend M Ibrahim; Iman Zarei; Erica C. Borresen; Lassina Doumbia; Abdoulaye Bore; Alima Cissoko; Seydou Douyon; Karim Kone; Johann Perez; Claudia Perez; Ann Hess; Zaid Abdo; Lansana Sangare; Ababacar Maiga; Sylvia Becker-Dreps; Lijuan Yuan; Ousmane Koita; Samuel Vilchez; Elizabeth P. Ryan; Hend Ibrahim. 2019. "Rice bran supplementation modulates growth, microbiome and metabolome in weaning infants: a clinical trial in Nicaragua and Mali." , no. : 530089.

Journal article
Published: 01 January 2019 in Integrative Food, Nutrition and Metabolism
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OA Text is an independent open-access scientific publisher showcases innovative research and ideas aimed at improving health by linking research and practice to the benefit of society.

ACS Style

Iman Zarei; Renee C Oppel; Erica C Borresen; Regina J Brown; Elizabeth P Ryan. Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran. Integrative Food, Nutrition and Metabolism 2019, 6, 1 .

AMA Style

Iman Zarei, Renee C Oppel, Erica C Borresen, Regina J Brown, Elizabeth P Ryan. Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran. Integrative Food, Nutrition and Metabolism. 2019; 6 (3):1.

Chicago/Turabian Style

Iman Zarei; Renee C Oppel; Erica C Borresen; Regina J Brown; Elizabeth P Ryan. 2019. "Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran." Integrative Food, Nutrition and Metabolism 6, no. 3: 1.

Randomized controlled trial
Published: 22 December 2018 in Nutrients
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Colorectal cancer (CRC) is the third leading cause of cancer-related death in the United States and emerging evidence supports that increased consumption of legumes, such as navy beans, can reduce risk. Navy bean consumption was previously shown to modulate host and microbiome metabolism, and this investigation was performed to assess the impact on the human stool metabolome, which includes the presence of navy bean metabolites. This 4-week, randomized-controlled trial with overweight and obese CRC survivors involved consumption of 1 meal and 1 snack daily. The intervention contained 35 g of cooked navy bean or macronutrient matched meals and snacks with 0 g of navy beans for the control group (n = 18). There were 30 statistically significant metabolite differences in the stool of participants that consumed navy bean at day 28 compared to the participants’ baseline (p ≤ 0.05) and 26 significantly different metabolites when compared to the control group. Of the 560 total metabolites identified from the cooked navy beans, there were 237 possible navy bean-derived metabolites that were identified in the stool of participants consuming navy beans, such as N-methylpipecolate, 2-aminoadipate, piperidine, and vanillate. The microbial metabolism of amino acids and fatty acids were also identified in stool after 4 weeks of navy bean intake including cadaverine, hydantoin-5 propionic acid, 4-hydroxyphenylacetate, and caprylate. The stool relative abundance of ophthalmate increased 5.25-fold for navy bean consumers that can indicate glutathione regulation, and involving cancer control mechanisms such as detoxification of xenobiotics, antioxidant defense, proliferation, and apoptosis. Metabolic pathways involving lysine, and phytochemicals were also modulated by navy bean intake in CRC survivors. These metabolites and metabolic pathways represent an acute response to increased navy bean intake, which merit further investigation for improving colonic health after long-term consumption.

ACS Style

Bridget A. Baxter; Renee C. Oppel; Elizabeth P. Ryan. Navy Beans Impact the Stool Metabolome and Metabolic Pathways for Colon Health in Cancer Survivors. Nutrients 2018, 11, 28 .

AMA Style

Bridget A. Baxter, Renee C. Oppel, Elizabeth P. Ryan. Navy Beans Impact the Stool Metabolome and Metabolic Pathways for Colon Health in Cancer Survivors. Nutrients. 2018; 11 (1):28.

Chicago/Turabian Style

Bridget A. Baxter; Renee C. Oppel; Elizabeth P. Ryan. 2018. "Navy Beans Impact the Stool Metabolome and Metabolic Pathways for Colon Health in Cancer Survivors." Nutrients 11, no. 1: 28.

Comparative study
Published: 01 December 2018 in Topics in Companion Animal Medicine
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The aim of this study was to compare fecal microbiome, plasma, fecal and urine metabolomes, and serum biochemistry of adult companion dogs according to body condition scores. Blood serum/plasma, urine, and fecal samples were collected from 66 clinically healthy, adult companion dogs of either normal weight (NW), overweight (OW), or obese dogs (OB). Analysis included fecal microbiome analysis via 16S ribosomal RNA gene amplicon sequencing, non-targeted plasma, fecal, and urine metabolomics using liquid chromatography/gas chromatography-mass spectrometry, and serum biochemistry for each dog. Few significant differences in serum biochemistry and fecal microbiome Operational Taxonomic Unit (OTU) were found between weight groups and there was high OTU variation between individual dogs. NW dogs had higher relative abundance of the genus Eubacterium (log-fold change 4.3, adjusted p-value = 0.003) and lower relative abundance of the family Bifidobacteriaceae (log-fold change -3.6, adjusted p-value = 0.02) compared to OB dogs. The microbiome of NW dogs had higher OTU richness compared with OB dogs. Metabolome analysis showed 185 plasma, 37 fecal, and 45 urine metabolites that significantly differed between NW and OW or OB dogs. There were notable significant differences in relative abundance of several plasma phospholipid moieties and fecal volatile fatty acids between weight phenotypes. The combinations of host and gut microbiota metabolic shifts suggest a pattern that could help detection of early metabolic changes in overweight dogs before the development of obesity related disease. The results of this study support the need for continued investigation into sensitive measures of metabolic aberrancies in overweight dogs.

ACS Style

Genevieve M. Forster; Jonathan Stockman; Noelle Noyes; Adam L. Heuberger; Corey Broeckling; Collin M. Bantle; Elizabeth P. Ryan. A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs. Topics in Companion Animal Medicine 2018, 33, 126 -135.

AMA Style

Genevieve M. Forster, Jonathan Stockman, Noelle Noyes, Adam L. Heuberger, Corey Broeckling, Collin M. Bantle, Elizabeth P. Ryan. A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs. Topics in Companion Animal Medicine. 2018; 33 (4):126-135.

Chicago/Turabian Style

Genevieve M. Forster; Jonathan Stockman; Noelle Noyes; Adam L. Heuberger; Corey Broeckling; Collin M. Bantle; Elizabeth P. Ryan. 2018. "A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs." Topics in Companion Animal Medicine 33, no. 4: 126-135.

Research article
Published: 09 November 2018 in PLOS ONE
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Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear. In this study, we systematically analyzed previously published 16S rRNA sequence data from CRC patients with matched tumor:tumor-adjacent biopsies (n = 294 pairs, n = 588 biospecimens) and matched tumor biopsy:fecal pairs (n = 42 pairs, n = 84 biospecimens). Procrustes analyses, random effects regression, random forest (RF) modeling, and inferred functional pathway analyses were conducted to assess community similarity and microbial diversity across heterogeneous patient groups and studies. Our results corroborate previously reported association of increased Fusobacterium with tumor biopsies. Parvimonas and Streptococcus abundances were also elevated while Faecalibacterium and Ruminococcaceae abundances decreased in tumors relative to tumor-adjacent biopsies and stool samples from the same case. With the exception of these limited taxa, the majority of findings from individual studies were not confirmed by other 16S rRNA gene-based datasets. RF models comparing tumor and tumor-adjacent specimens yielded an area under curve (AUC) of 64.3%, and models of tumor biopsies versus fecal specimens exhibited an AUC of 82.5%. Although some taxa were shared between fecal and tumor samples, their relative abundances varied substantially. Inferred functional analysis identified potential differences in branched amino acid and lipid metabolism. Microbial markers that reliably occur in tumor tissue can have implications for microbiome based and microbiome targeting therapeutics for CRC.

ACS Style

Manasi S. Shah; Todd DeSantis; Jose-Miguel Yamal; Tiffany Weir; Elizabeth P. Ryan; Julia L. Cope; Emily B. Hollister. Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. PLOS ONE 2018, 13, e0207002 .

AMA Style

Manasi S. Shah, Todd DeSantis, Jose-Miguel Yamal, Tiffany Weir, Elizabeth P. Ryan, Julia L. Cope, Emily B. Hollister. Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. PLOS ONE. 2018; 13 (11):e0207002.

Chicago/Turabian Style

Manasi S. Shah; Todd DeSantis; Jose-Miguel Yamal; Tiffany Weir; Elizabeth P. Ryan; Julia L. Cope; Emily B. Hollister. 2018. "Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer." PLOS ONE 13, no. 11: e0207002.